[BioC] GWATools use in creating ncdf files

Stephanie M. Gogarten sdmorris at u.washington.edu
Mon Jul 8 21:51:53 CEST 2013


Hi Sam,

I haven't seen this error before.  The relevant bit of code is this:

dat$geno <- paste(dat$a1,dat$a2,sep="")
new.names <- names(dat)[!is.element(names(dat),c("a1","a2"))]
dat <- dat[,new.names]

"dat" is the data.frame read from your FinalReport file.  "a1" and "a2" 
columns are the two alleles, specified in the col.nums argument.  If the 
data file had columns for "a1" and "a2" but not "geno," the code pastes 
"a1" and "a2" together to make a "geno" column, then removes the "a1" 
and "a2" columns.  I don't know how "new.names" can contain invalid 
columns, since it should be a subset of the original column names.

Maybe double check your values for col.nums?  Otherwise the only way I 
can think to debug is to step through the code for ncdfAddData and see 
what's happening at this part.  I could do that if you could send me the 
relevant file, but I'm guessing you can't do that for security reasons, 
so maybe you could try it.

Stephanie

On 7/3/13 12:59 PM, Sam Rose wrote:
> Hi Stephanie,
>
> Quick question, do you have any experience with the following error in
> the ncdfAddData() function?
> Error in `[.data.frame`(dat, , new.names) : undefined columns selected
>  > traceback()
> 4: stop("undefined columns selected")
> 3: `[.data.frame`(dat, , new.names)
> 2: dat[, new.names]
> 1: ncdfAddData(path = ".", ncdf.filename = geno.nc.file, snp.annotation
> = snp.annot,
>         scan.annotation = scan.annot, sep.type = "\t", skip.num = 1,
>         col.total = 16, col.nums = col.nums, scan.name.in.file = 0)
>
> I am using a new data set exactly the same as the last one which worked
> and can't seem to figure out the problem behind this one.
>
> These are what the tops of my scan and snp annotation files look like:
> snp:
> snpID   chromosome      position        rsID
> 1       1       72017   rs4477212
> 2       1       524110  SNP1-524110
> 3       1       555149  SNP1-555149
> 4       1       559487  SNP1-559487
> 5       1       679049  rs4000335
> 6       1       713781  SNP1-713781
> 7       1       719495  SNP1-719495
> 8       1       742429  rs3094315
> 9       1       742584  rs3131972
>
> scan:
> scanID  subjectID       genoRunID       sex     file
> 2       PT-JOPP 5491005008_R03C01       M
> 5491005008_R03C01.gtc.txt.use
> 3       PT-JOQ4 5434246116_R01C01       F
> 5434246116_R01C01.gtc.txt.use
> 4       PT-JOQ6 5491005134_R03C01       M
> 5491005134_R03C01.gtc.txt.use
> 5       PT-JOQB 5434078047_R04C01       F
> 5434078047_R04C01.gtc.txt.use
> 6       PT-JOQG 5491005152_R03C01       F
> 5491005152_R03C01.gtc.txt.use
> 7       PT-JOP2 5434246116_R03C01       F
> 5434246116_R03C01.gtc.txt.use
> 8       PT-JOQI 5491005134_R04C01       M
> 5491005134_R04C01.gtc.txt.use
> 9       PT-JOQL 5434246084_R04C01       M
> 5434246084_R04C01.gtc.txt.use
> 11      PT-JOQW 5491005061_R02C01       M
> 5491005061_R02C01.gtc.txt.use
>
> Any help would be appreciated.
>
> Thanks,
> Sam
>
>
>
> On Wed, Jun 12, 2013 at 9:45 AM, Sam Rose <srose at broadinstitute.org
> <mailto:srose at broadinstitute.org>> wrote:
>
>     Hi Stephanie,
>
>     After using your commands I was able to successfully use the package
>     without error. I think the error was within the column names, which
>     needed to be changed from genoRunID to scanID in order to be
>     recognized by the later  commands.
>
>     Thanks for all of your help it was very much appreciated.
>
>     Best,
>     Sam
>
>
>     On Fri, Jun 7, 2013 at 3:27 PM, Stephanie M. Gogarten
>     <sdmorris at u.washington.edu <mailto:sdmorris at u.washington.edu>> wrote:
>
>         Hi Sam,
>
>         I can't reproduce your error using the data you sent.  Either
>         you had an error in creating your netCDF files, or the sample
>         you were working with doesn't have any usable data.  Below is
>         the code I used; see if you can reproduce it with your other sample.
>
>         library(GWASTools)
>
>         scan.annot <-
>         read.table("8850270138_R01C01.__gtc.txt.scan_annotation",
>                                   colClasses=c("integer",
>         rep("character",4)),
>                                   header=TRUE)
>         scanAnnot <- ScanAnnotationDataFrame(scan.__annot)
>
>         snp.annot <-
>         read.table("8850270138_R01C01.__gtc.txt.snp_annotation",
>         as.is <http://as.is>=TRUE, header=TRUE)
>         snpAnnot <- SnpAnnotationDataFrame(snp.__annot)
>
>         geno.nc.file <- "geno.nc <http://geno.nc>"
>         ncdfCreate(ncdf.filename=geno.__nc.file, snp.annotation=snp.annot,
>                     variables="genotype", n.samples=1, precision="single")
>         names(scan.annot)[3] <- "scanName"
>         names(snp.annot)[4] <- "snpName"
>         col.nums <- as.integer(c(1,7,8))
>         names(col.nums) <- c("snp","a1","a2")
>         ncdfAddData(path=".", ncdf.filename=geno.nc.file,
>                      snp.annotation=snp.annot,
>                      scan.annotation=scan.annot,
>                      sep.type="\t", skip.num=1,
>                      col.total=16, col.nums=col.nums,
>                      scan.name.in.file=0)
>
>         bl.nc.file <- "bl.nc <http://bl.nc>"
>         ncdfCreate(ncdf.filename=bl.__nc.file, snp.annotation=snp.annot,
>                     variables=c("BAlleleFreq", "LogRRatio"),
>                     n.samples=1, precision="single")
>         col.nums <- as.integer(c(1,15,16))
>         names(col.nums) <- c("snp", "ballelefreq", "logrratio")
>         ncdfAddData(path=".", ncdf.filename=bl.nc.file,
>                      snp.annotation=snp.annot,
>                      scan.annotation=scan.annot,
>                      sep.type="\t", skip.num=1,
>                      col.total=16, col.nums=col.nums,
>                      scan.name.in.file=0)
>
>         genoData <- GenotypeData(__NcdfGenotypeReader(geno.nc
>         <http://geno.nc>.__file),
>                                   scanAnnot=scanAnnot, snpAnnot=snpAnnot)
>         blData <- IntensityData(__NcdfIntensityReader(bl.nc
>         <http://bl.nc>.__file),
>                                  scanAnnot=scanAnnot, snpAnnot=snpAnnot)
>
>         scan.ids <- read.table("scan.ids")[,1]
>         snp.ids <- read.table("snp.ids")[,1]
>         chrom.ids <- read.table("chrom.ids")[,1]
>         seg <- anomSegmentBAF(blData, genoData, scan.ids=scan.ids,
>                                chrom.ids=chrom.ids, snp.ids=snp.ids)
>         head(seg)
>            scanID chromosome left.index right.index num.mark seg.mean
>         1      1          1          5       59479    17205   0.1582
>         2      1          2      59498      117436    17360   0.1596
>         3      1          3     117437      164865    14181   0.1595
>         4      1          4     164872      205472    12218   0.1640
>         5      1          5     205474      247715    13313   0.1602
>         6      1          6     247752      296212    15232   0.1629
>
>         best wishes,
>         Stephanie
>
>         On 6/6/13 1:28 PM, Sam Rose wrote:
>
>             Hi Stephanie,
>
>             I am providing a CEU control sample data from the same
>             study, NA12878. I
>             just sent it to you in a dropbox link. Let me know if there
>             are any
>             questions.
>
>             Best,
>             Sam
>
>
>
>
>             On Wed, Jun 5, 2013 at 12:11 PM, Stephanie M. Gogarten
>             <sdmorris at u.washington.edu
>             <mailto:sdmorris at u.washington.edu>
>             <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>> wrote:
>
>                  It's not finding any BAF values that meet all the
>             criteria (snpID in
>                  "snp.ids", chromosome in "chrom.ids", genotype is
>             heterozygous or
>                  missing, BAF is non-missing).
>
>                  Is it possible for you to send me the data you're
>             using, along with
>                  your values of "scan.ids", "chrom.ids", and "snp.ids"?
>
>                  Stephanie
>
>
>                  On 6/4/13 2:23 PM, Sam Rose wrote:
>
>                      Yes this was intentional. I just wanted to get it
>             running for
>                      one sample
>                      and then expand to the rest. I was also limiting
>             this to only
>                      autosomes
>                      for the time being.
>
>                      This is the error message I get now:
>
>                        > seg <- anomSegmentBAF(blData, genoData,
>             scan.ids=scan.ids,
>                      +                            chrom.ids=chrom.ids,
>             snp.ids=snp.ids)
>                      Error in anomSegmentBAF(blData, genoData, scan.ids
>             = scan.ids,
>                      chrom.ids
>                      = chrom.ids,  :
>                          no valid BAF values for chromosomes in chrom.ids
>
>                      Hopefully this helps.
>
>                      Best,
>                      Sam
>
>
>                      On Tue, Jun 4, 2013 at 12:28 AM, Stephanie M. Gogarten
>                      <sdmorris at u.washington.edu
>             <mailto:sdmorris at u.washington.edu>
>             <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>
>                      <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>> wrote:
>
>                           You have only one sample in your netCDF files
>             - is this
>                      intentional?
>
>                           That should not cause your error, however.
>               Can you try
>                      running with
>                           the latest GWASTools version and tell me what
>             the new error
>                      message is?
>
>                           Also, you should include in your scan annotation a
>                      character vector
>                           "sex" with values of "M" or "F".  The code
>             treats males and
>                      females
>                           differently for X chromosome SNPs, and will
>             complain later
>                      if this
>                           variable is missing.
>
>                           Stephanie
>
>
>                           On 6/3/13 4:04 PM, Sam Rose wrote:
>
>                               After checking again it still isn't quite
>             working.
>
>                               I am pasting below the str() results for
>             my intensity
>                      and genotype
>                               objects, maybe something in this can point
>             clearly to
>                      what I am
>                               doing
>                               wrong.
>
>                               I am using an integer vector of 1 to the
>             total number
>                      of snps
>                               for my snp
>                               id since it gave me some trouble before
>             when it wasn't
>                      sorted.
>
>                               Best,
>                               Sam
>
>                                 > str(genoData)
>                               Formal class 'GenotypeData' [package
>             "GWASTools"] with
>                      3 slots
>                                   ..@ data     :Formal class
>             'NcdfGenotypeReader'
>                      [package
>                               "GWASTools"]
>                               with 13 slots
>                                   .. .. ..@ snpDim       : chr "snp"
>                                   .. .. ..@ scanDim      : chr "sample"
>                                   .. .. ..@ snpIDvar     : chr "snp"
>                                   .. .. ..@ chromosomeVar: chr "chromosome"
>                                   .. .. ..@ positionVar  : chr "position"
>                                   .. .. ..@ scanIDvar    : chr "sampleID"
>                                   .. .. ..@ genotypeVar  : chr "genotype"
>                                   .. .. ..@ XchromCode   : int 23
>                                   .. .. ..@ YchromCode   : int 25
>                                   .. .. ..@ XYchromCode  : int 24
>                                   .. .. ..@ MchromCode   : int 26
>                                   .. .. ..@ filename     : chr
>             "tmp.geno.skea.nc <http://tmp.geno.skea.nc>
>                      <http://tmp.geno.skea.nc>
>                               <http://tmp.geno.skea.nc>
>             <http://tmp.geno.skea.nc>"
>
>
>                                   .. .. ..@ handler      :List of 10
>                                   .. .. .. ..$ id          : int 524288
>                                   .. .. .. ..$ ndims       : int 2
>                                   .. .. .. ..$ natts       : int 2
>                                   .. .. .. ..$ unlimdimid  : num 1
>                                   .. .. .. ..$ filename    : chr
>             "tmp.geno.skea.nc <http://tmp.geno.skea.nc>
>                      <http://tmp.geno.skea.nc>
>                               <http://tmp.geno.skea.nc>
>                               <http://tmp.geno.skea.nc>"
>
>                                   .. .. .. ..$ varid2Rindex: num [1:6] 0
>             1 0 2 3 4
>                                   .. .. .. ..$ writable    : logi FALSE
>                                   .. .. .. ..$ dim         :List of 2
>                                   .. .. .. .. ..$ sample:List of 8
>                                   .. .. .. .. .. ..$ name         : chr
>             "sample"
>                                   .. .. .. .. .. ..$ len          : int 1
>                                   .. .. .. .. .. ..$ unlim        : logi
>             TRUE
>                                   .. .. .. .. .. ..$ id           : int 1
>                                   .. .. .. .. .. ..$ dimvarid     : num 1
>                                   .. .. .. .. .. ..$ units        : chr
>             "count"
>                                   .. .. .. .. .. ..$ vals         : logi NA
>                                   .. .. .. .. .. ..$ create_dimvar: logi
>             TRUE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "dim.ncdf"
>                                   .. .. .. .. ..$ snp   :List of 8
>                                   .. .. .. .. .. ..$ name         : chr
>             "snp"
>                                   .. .. .. .. .. ..$ len          : int
>             709358
>                                   .. .. .. .. .. ..$ unlim        : logi
>             FALSE
>                                   .. .. .. .. .. ..$ id           : int 2
>                                   .. .. .. .. .. ..$ dimvarid     : num 3
>                                   .. .. .. .. .. ..$ units        : chr
>             "count"
>                                   .. .. .. .. .. ..$ vals         : int
>                      [1:709358(1d)] 1 2 3 4
>                               5 6 7 8
>                               9 10 ...
>                                   .. .. .. .. .. ..$ create_dimvar: logi
>             TRUE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "dim.ncdf"
>                                   .. .. .. ..$ nvars       : num 4
>                                   .. .. .. ..$ var         :List of 4
>                                   .. .. .. .. ..$ sampleID  :List of 16
>                                   .. .. .. .. .. ..$ id          : int 2
>                                   .. .. .. .. .. ..$ name        : chr
>             "sampleID"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int 1
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 1
>                                   .. .. .. .. .. ..$ units       : chr "id"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "sampleID"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "sample"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 1
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi TRUE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 1
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 1
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : logi NA
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int 1
>                                   .. .. .. .. .. ..$ unlim       : logi TRUE
>                                   .. .. .. .. .. ..$ missval     : int 0
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ position  :List of 16
>                                   .. .. .. .. .. ..$ id          : int 4
>                                   .. .. .. .. .. ..$ name        : chr
>             "position"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             709358
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 2
>                                   .. .. .. .. .. ..$ units       : chr
>             "bases"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "position"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             709358
>                                   .. .. .. .. .. ..$ unlim       : logi
>             FALSE
>                                   .. .. .. .. .. ..$ missval     : int -1
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ chromosome:List of 16
>                                   .. .. .. .. .. ..$ id          : int 5
>                                   .. .. .. .. .. ..$ name        : chr
>             "chromosome"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             709358
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 2
>                                   .. .. .. .. .. ..$ units       : chr "id"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "chromosome"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             709358
>                                   .. .. .. .. .. ..$ unlim       : logi
>             FALSE
>                                   .. .. .. .. .. ..$ missval     : int -1
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ genotype  :List of 16
>                                   .. .. .. .. .. ..$ id          : int 6
>                                   .. .. .. .. .. ..$ name        : chr
>             "genotype"
>                                   .. .. .. .. .. ..$ ndims       : int 2
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ prec        : chr
>             "byte"
>                                   .. .. .. .. .. ..$ dimids      : num
>             [1:2] 2 1
>                                   .. .. .. .. .. ..$ units       : chr
>             "num_A_alleles"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "genotype"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 2
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "sample"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 1
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi TRUE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 1
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 1
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : logi NA
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ unlim       : logi TRUE
>                                   .. .. .. .. .. ..$ missval     : int -1
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. ..- attr(*, "class")= chr "ncdf"
>                                   ..@ snpAnnot :Formal class
>             'SnpAnnotationDataFrame'
>                      [package
>                               "GWASTools"] with 11 slots
>                                   .. .. ..@ idCol            : chr "snpID"
>                                   .. .. ..@ chromosomeCol    : chr
>             "chromosome"
>                                   .. .. ..@ positionCol      : chr
>             "position"
>                                   .. .. ..@ XchromCode       : int 23
>                                   .. .. ..@ YchromCode       : int 25
>                                   .. .. ..@ XYchromCode      : int 24
>                                   .. .. ..@ MchromCode       : int 26
>                                   .. .. ..@ varMetadata
>               :'data.frame':     4
>                      obs. of  1
>                               variable:
>                                   .. .. .. ..$ labelDescription: chr
>             [1:4] NA NA NA NA
>                                   .. .. ..@ data             :'data.frame':
>                      709358 obs. of  4
>                               variables:
>                                   .. .. .. ..$ snpID     : int
>             [1:709358] 1 2 3 4 5 6
>                      7 8 9 10 ...
>                                   .. .. .. ..$ chromosome: int
>             [1:709358] 1 1 1 1 1 1
>                      1 1 1 1 ...
>                                   .. .. .. ..$ position  : int
>             [1:709358] 82154
>                      752566 752721
>                               768448
>                               776546 798959 800007 838555 846808 854250 ...
>                                   .. .. .. ..$ rsID      : Factor w/
>             709358 levels
>                               "rs1000000","rs1000002",..: 444820 394558
>             397236 154397
>                      130894 89309
>                               528142 485618 444755 595849 ...
>                                   .. .. ..@ dimLabels        : chr [1:2]
>             "snps"
>                      "variables"
>                                   .. .. ..@ .__classVersion__:Formal
>             class 'Versions'
>                      [package
>                               "Biobase"] with 1 slots
>                                   .. .. .. .. ..@ .Data:List of 1
>                                   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>                                   ..@ scanAnnot:Formal class
>                      'ScanAnnotationDataFrame' [package
>                               "GWASTools"] with 6 slots
>                                   .. .. ..@ idCol            : chr "scanID"
>                                   .. .. ..@ sexCol           : chr "sex"
>                                   .. .. ..@ varMetadata
>               :'data.frame':     4
>                      obs. of  1
>                               variable:
>                                   .. .. .. ..$ labelDescription: chr
>             [1:4] NA NA NA NA
>                                   .. .. ..@ data
>             :'data.frame':     1
>                      obs. of  4
>                               variables:
>                                   .. .. .. ..$ scanID   : int 1
>                                   .. .. .. ..$ subjectID: Factor w/ 1
>             level "PT-PTWN": 1
>                                   .. .. .. ..$ genoRunID: Factor w/ 1 level
>                      "8820505004_R01C01": 1
>                                   .. .. .. ..$ file     : Factor w/ 1 level
>                               "8820505004_R01C01.gtc.txt.______use": 1
>
>                                   .. .. ..@ dimLabels        : chr [1:2]
>             "scans"
>                      "variables"
>                                   .. .. ..@ .__classVersion__:Formal
>             class 'Versions'
>                      [package
>                               "Biobase"] with 1 slots
>                                   .. .. .. .. ..@ .Data:List of 1
>                                   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>                                 > str(blData)
>                               Formal class 'IntensityData' [package
>             "GWASTools"] with
>                      3 slots
>                                   ..@ data     :Formal class
>             'NcdfIntensityReader'
>                      [package
>                               "GWASTools"] with 17 slots
>                                   .. .. ..@ snpDim       : chr "snp"
>                                   .. .. ..@ scanDim      : chr "sample"
>                                   .. .. ..@ snpIDvar     : chr "snp"
>                                   .. .. ..@ chromosomeVar: chr "chromosome"
>                                   .. .. ..@ positionVar  : chr "position"
>                                   .. .. ..@ scanIDvar    : chr "sampleID"
>                                   .. .. ..@ qualityVar   : chr "quality"
>                                   .. .. ..@ xVar         : chr "X"
>                                   .. .. ..@ yVar         : chr "Y"
>                                   .. .. ..@ bafVar       : chr "BAlleleFreq"
>                                   .. .. ..@ lrrVar       : chr "LogRRatio"
>                                   .. .. ..@ XchromCode   : int 23
>                                   .. .. ..@ YchromCode   : int 25
>                                   .. .. ..@ XYchromCode  : int 24
>                                   .. .. ..@ MchromCode   : int 26
>                                   .. .. ..@ filename     : chr
>             "tmp.baf.skea.nc <http://tmp.baf.skea.nc>
>                      <http://tmp.baf.skea.nc>
>                               <http://tmp.baf.skea.nc>
>             <http://tmp.baf.skea.nc>"
>
>
>                                   .. .. ..@ handler      :List of 10
>                                   .. .. .. ..$ id          : int 458752
>                                   .. .. .. ..$ ndims       : int 2
>                                   .. .. .. ..$ natts       : int 2
>                                   .. .. .. ..$ unlimdimid  : num 1
>                                   .. .. .. ..$ filename    : chr
>             "tmp.baf.skea.nc <http://tmp.baf.skea.nc>
>                      <http://tmp.baf.skea.nc>
>                               <http://tmp.baf.skea.nc>
>             <http://tmp.baf.skea.nc>"
>
>
>                                   .. .. .. ..$ varid2Rindex: num [1:7] 0
>             1 0 2 3 4 5
>                                   .. .. .. ..$ writable    : logi FALSE
>                                   .. .. .. ..$ dim         :List of 2
>                                   .. .. .. .. ..$ sample:List of 8
>                                   .. .. .. .. .. ..$ name         : chr
>             "sample"
>                                   .. .. .. .. .. ..$ len          : int 1
>                                   .. .. .. .. .. ..$ unlim        : logi
>             TRUE
>                                   .. .. .. .. .. ..$ id           : int 1
>                                   .. .. .. .. .. ..$ dimvarid     : num 1
>                                   .. .. .. .. .. ..$ units        : chr
>             "count"
>                                   .. .. .. .. .. ..$ vals         : logi NA
>                                   .. .. .. .. .. ..$ create_dimvar: logi
>             TRUE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "dim.ncdf"
>                                   .. .. .. .. ..$ snp   :List of 8
>                                   .. .. .. .. .. ..$ name         : chr
>             "snp"
>                                   .. .. .. .. .. ..$ len          : int
>             709358
>                                   .. .. .. .. .. ..$ unlim        : logi
>             FALSE
>                                   .. .. .. .. .. ..$ id           : int 2
>                                   .. .. .. .. .. ..$ dimvarid     : num 3
>                                   .. .. .. .. .. ..$ units        : chr
>             "count"
>                                   .. .. .. .. .. ..$ vals         : int
>                      [1:709358(1d)] 1 2 3 4
>                               5 6 7 8
>                               9 10 ...
>                                   .. .. .. .. .. ..$ create_dimvar: logi
>             TRUE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "dim.ncdf"
>                                   .. .. .. ..$ nvars       : num 5
>                                   .. .. .. ..$ var         :List of 5
>                                   .. .. .. .. ..$ sampleID   :List of 16
>                                   .. .. .. .. .. ..$ id          : int 2
>                                   .. .. .. .. .. ..$ name        : chr
>             "sampleID"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int 1
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 1
>                                   .. .. .. .. .. ..$ units       : chr "id"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "sampleID"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "sample"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 1
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi TRUE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 1
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 1
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : logi NA
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int 1
>                                   .. .. .. .. .. ..$ unlim       : logi TRUE
>                                   .. .. .. .. .. ..$ missval     : int 0
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ position   :List of 16
>                                   .. .. .. .. .. ..$ id          : int 4
>                                   .. .. .. .. .. ..$ name        : chr
>             "position"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             709358
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 2
>                                   .. .. .. .. .. ..$ units       : chr
>             "bases"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "position"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             709358
>                                   .. .. .. .. .. ..$ unlim       : logi
>             FALSE
>                                   .. .. .. .. .. ..$ missval     : int -1
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ chromosome :List of 16
>                                   .. .. .. .. .. ..$ id          : int 5
>                                   .. .. .. .. .. ..$ name        : chr
>             "chromosome"
>                                   .. .. .. .. .. ..$ ndims       : int 1
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             709358
>                                   .. .. .. .. .. ..$ prec        : chr "int"
>                                   .. .. .. .. .. ..$ dimids      : num 2
>                                   .. .. .. .. .. ..$ units       : chr "id"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "chromosome"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 1
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             709358
>                                   .. .. .. .. .. ..$ unlim       : logi
>             FALSE
>                                   .. .. .. .. .. ..$ missval     : int -1
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ BAlleleFreq:List of 16
>                                   .. .. .. .. .. ..$ id          : int 6
>                                   .. .. .. .. .. ..$ name        : chr
>             "BAlleleFreq"
>                                   .. .. .. .. .. ..$ ndims       : int 2
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ prec        : chr
>             "float"
>                                   .. .. .. .. .. ..$ dimids      : num
>             [1:2] 2 1
>                                   .. .. .. .. .. ..$ units       : chr
>             "intensity"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "BAlleleFreq"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 2
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "sample"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 1
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi TRUE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 1
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 1
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : logi NA
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ unlim       : logi TRUE
>                                   .. .. .. .. .. ..$ missval     : num -9999
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. .. ..$ LogRRatio  :List of 16
>                                   .. .. .. .. .. ..$ id          : int 7
>                                   .. .. .. .. .. ..$ name        : chr
>             "LogRRatio"
>                                   .. .. .. .. .. ..$ ndims       : int 2
>                                   .. .. .. .. .. ..$ natts       : int 2
>                                   .. .. .. .. .. ..$ size        : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ prec        : chr
>             "float"
>                                   .. .. .. .. .. ..$ dimids      : num
>             [1:2] 2 1
>                                   .. .. .. .. .. ..$ units       : chr
>             "intensity"
>                                   .. .. .. .. .. ..$ longname    : chr
>             "LogRRatio"
>                                   .. .. .. .. .. ..$ dims        : list()
>                                   .. .. .. .. .. ..$ dim         :List of 2
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "snp"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 709358
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi FALSE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 2
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 3
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : int
>                      [1:709358(1d)] 1
>                               2 3 4 5
>                               6 7 8 9 10 ...
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. .. ..$ :List of 8
>                                   .. .. .. .. .. .. .. ..$ name
>             : chr "sample"
>                                   .. .. .. .. .. .. .. ..$ len
>               : int 1
>                                   .. .. .. .. .. .. .. ..$ unlim
>               : logi TRUE
>                                   .. .. .. .. .. .. .. ..$ id
>             : int 1
>                                   .. .. .. .. .. .. .. ..$ dimvarid
>             : num 1
>                                   .. .. .. .. .. .. .. ..$ units
>               : chr "count"
>                                   .. .. .. .. .. .. .. ..$ vals
>             : logi NA
>                                   .. .. .. .. .. .. .. ..$
>             create_dimvar: logi TRUE
>                                   .. .. .. .. .. .. .. ..- attr(*,
>             "class")= chr
>                      "dim.ncdf"
>                                   .. .. .. .. .. ..$ varsize     : int
>             [1:2] 709358 1
>                                   .. .. .. .. .. ..$ unlim       : logi TRUE
>                                   .. .. .. .. .. ..$ missval     : num -9999
>                                   .. .. .. .. .. ..$ hasAddOffset: logi
>             FALSE
>                                   .. .. .. .. .. ..$ hasScaleFact: logi
>             FALSE
>                                   .. .. .. .. .. ..- attr(*, "class")=
>             chr "var.ncdf"
>                                   .. .. .. ..- attr(*, "class")= chr "ncdf"
>                                   ..@ snpAnnot :Formal class
>             'SnpAnnotationDataFrame'
>                      [package
>                               "GWASTools"] with 11 slots
>                                   .. .. ..@ idCol            : chr "snpID"
>                                   .. .. ..@ chromosomeCol    : chr
>             "chromosome"
>                                   .. .. ..@ positionCol      : chr
>             "position"
>                                   .. .. ..@ XchromCode       : int 23
>                                   .. .. ..@ YchromCode       : int 25
>                                   .. .. ..@ XYchromCode      : int 24
>                                   .. .. ..@ MchromCode       : int 26
>                                   .. .. ..@ varMetadata
>               :'data.frame':     4
>                      obs. of  1
>                               variable:
>                                   .. .. .. ..$ labelDescription: chr
>             [1:4] NA NA NA NA
>                                   .. .. ..@ data             :'data.frame':
>                      709358 obs. of  4
>                               variables:
>                                   .. .. .. ..$ snpID     : int
>             [1:709358] 1 2 3 4 5 6
>                      7 8 9 10 ...
>                                   .. .. .. ..$ chromosome: int
>             [1:709358] 1 1 1 1 1 1
>                      1 1 1 1 ...
>                                   .. .. .. ..$ position  : int
>             [1:709358] 82154
>                      752566 752721
>                               768448
>                               776546 798959 800007 838555 846808 854250 ...
>                                   .. .. .. ..$ rsID      : Factor w/
>             709358 levels
>                               "rs1000000","rs1000002",..: 444820 394558
>             397236 154397
>                      130894 89309
>                               528142 485618 444755 595849 ...
>                                   .. .. ..@ dimLabels        : chr [1:2]
>             "snps"
>                      "variables"
>                                   .. .. ..@ .__classVersion__:Formal
>             class 'Versions'
>                      [package
>                               "Biobase"] with 1 slots
>                                   .. .. .. .. ..@ .Data:List of 1
>                                   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>                                   ..@ scanAnnot:Formal class
>                      'ScanAnnotationDataFrame' [package
>                               "GWASTools"] with 6 slots
>                                   .. .. ..@ idCol            : chr "scanID"
>                                   .. .. ..@ sexCol           : chr "sex"
>                                   .. .. ..@ varMetadata
>               :'data.frame':     4
>                      obs. of  1
>                               variable:
>                                   .. .. .. ..$ labelDescription: chr
>             [1:4] NA NA NA NA
>                                   .. .. ..@ data
>             :'data.frame':     1
>                      obs. of  4
>                               variables:
>                                   .. .. .. ..$ scanID   : int 1
>                                   .. .. .. ..$ subjectID: Factor w/ 1
>             level "PT-PTWN": 1
>                                   .. .. .. ..$ genoRunID: Factor w/ 1 level
>                      "8820505004_R01C01": 1
>                                   .. .. .. ..$ file     : Factor w/ 1 level
>                               "8820505004_R01C01.gtc.txt.______use": 1
>
>                                   .. .. ..@ dimLabels        : chr [1:2]
>             "scans"
>                      "variables"
>                                   .. .. ..@ .__classVersion__:Formal
>             class 'Versions'
>                      [package
>                               "Biobase"] with 1 slots
>                                   .. .. .. .. ..@ .Data:List of 1
>                                   .. .. .. .. .. ..$ : int [1:3] 1 1 0
>
>
>
>                               On Fri, May 31, 2013 at 2:41 PM, Sam Rose
>                               <srose at broadinstitute.org
>             <mailto:srose at broadinstitute.org>
>                      <mailto:srose at broadinstitute.__org
>             <mailto:srose at broadinstitute.org>>
>                      <mailto:srose at broadinstitute.
>             <mailto:srose at broadinstitute.>____org
>                      <mailto:srose at broadinstitute.__org
>             <mailto:srose at broadinstitute.org>>>
>                               <mailto:srose at broadinstitute
>             <mailto:srose at broadinstitute>.
>                      <mailto:srose at broadinstitute
>             <mailto:srose at broadinstitute>.>______org
>
>                               <mailto:srose at broadinstitute.
>             <mailto:srose at broadinstitute.>____org
>                      <mailto:srose at broadinstitute.__org
>             <mailto:srose at broadinstitute.org>>>>> wrote:
>
>                                    Looks like there was some problems
>             reading the
>                      file in on
>                               my end,
>                                    some chromosomes didn't make it in
>             probably from a
>                               preprocessing
>                                    step on my end. I'll let you know if
>             I can't rectify.
>
>                                    Thanks again for the help,
>
>                                    Sam
>
>
>                                    On Thu, May 30, 2013 at 4:43 PM,
>             Stephanie M. Gogarten
>                                    <sdmorris at u.washington.edu
>             <mailto:sdmorris at u.washington.edu>
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>
>                               <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>
>                               <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.
>                      <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.__>____edu
>                               <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>>> wrote:
>
>                                        Hi Sam,
>
>                                        I need to add a more informative
>             error message
>                      - the
>                               problem is
>                                        that no valid BAF values are
>             reaching the call
>                      to CNA
>                               (baf.dat
>                                        is NULL).  This could happen if
>             the values of
>                      snp.ids or
>                                        chrom.ids are invalid - these
>             should all be
>                      integer values
>                                        matching the contents of snpID
>             and chromosome
>                      in the netCDF
>                                        file.  What values are you using
>             for these
>                      arguments?
>
>                                        You will need to have LRR in the
>             intensity
>                      NetCDF file.  A
>                                        portion of the code downstream
>             from the error
>                      you're
>                               getting
>                                        uses LRR to filter potential
>             anomalies.
>
>                                        Stephanie
>
>
>                                        On 5/30/13 12:30 PM, Sam Rose wrote:
>
>                                            Thank you for your previous
>             help Stephanie.
>
>                                            I am afraid I have another
>             problem I can't
>                      seem to
>                               work out.
>
>                                            I have gotten as far as
>             reading in the
>                      BAlleleFreq
>                               and Geno
>                                            files into
>                                            their respective ncdf
>             formats. I only have
>                      the baf
>                               data in
>                                            the intensity
>                                            ncdf file, do I need LRR too?
>             When I run the
>                               anomDetectBAF()
>                                            function it
>                                            gives me this error:
>
>                                              > anom <-
>             anomDetectBAF(blData, genoData,
>                               scan.ids=scan.ids,
>                                            chrom.ids=chrom.ids,
>             snp.ids=snp.ids,
>                                            centromere=centromeres.hg19)
>                                            Error in
>             CNA(as.vector(baf.dat), chr, index,
>                               data.type =
>                                            "logratio",
>                                            sampleid = snum) :
>                                                genomdat must be numeric
>
>                                            I have checked and the data
>             that I put in
>                      to the
>                               genotype
>                                            data file was
>                                            numeric and present as well
>             as the baf
>                      data. I'm
>                               wondering
>                                            if you have
>                                            seen this error before and
>             may potentially
>                      know
>                               what I can
>                                            do to rectify?
>
>                                            Thanks,
>                                            Sam
>
>
>                                            On Wed, Apr 24, 2013 at 12:01 AM,
>                      Stephanie M. Gogarten
>                                            <sdmorris at u.washington.edu
>             <mailto:sdmorris at u.washington.edu>
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>
>                               <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>
>                                            <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.
>                      <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.__>____edu
>                               <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>>
>                                            <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>
>                      <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>>__.
>                               <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>
>                      <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>>__.__>____edu
>
>
>                                            <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.
>                      <mailto:sdmorris at u.washington
>             <mailto:sdmorris at u.washington>.__>____edu
>                               <mailto:sdmorris at u.washington.
>             <mailto:sdmorris at u.washington.>____edu
>                      <mailto:sdmorris at u.washington.__edu
>             <mailto:sdmorris at u.washington.edu>>>>>> wrote:
>
>                                                 Hi Sam,
>
>                                                 Section 2 of the
>             vignette "GWAS Data
>                      Cleaning"
>                               contains
>                                            an example
>                                                 of how to import raw
>             illumina data of
>                      exactly
>                               this type
>                                            into
>                                                 GWASTools. The example
>             data is
>                      contained in
>                               the package
>                                            "GWASdata."
>
>                                                 If you have any further
>             questions after
>                               reading the
>                                            vignette, please
>                                                 cc the bioconductor
>             mailing list
>                                            (bioconductor at r-project.org
>             <mailto:bioconductor at r-project.org>
>                      <mailto:bioconductor at r-__project.org
>             <mailto:bioconductor at r-project.org>>
>                               <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>
>                      <mailto:bioconductor at r-__project.org
>             <mailto:bioconductor at r-project.org>>>
>                               <mailto:bioconductor at r-______project.org
>             <mailto:bioconductor at r-____project.org>
>                      <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>>
>                               <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>
>                      <mailto:bioconductor at r-__project.org
>             <mailto:bioconductor at r-project.org>>>>
>
>                      <mailto:bioconductor at r-________project.org
>             <mailto:bioconductor at r-______project.org>
>                      <mailto:bioconductor at r-______project.org
>             <mailto:bioconductor at r-____project.org>>
>                               <mailto:bioconductor at r-______project.org
>             <mailto:bioconductor at r-____project.org>
>                      <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>>>
>
>
>
>             <mailto:bioconductor at r-______project.org
>             <mailto:bioconductor at r-____project.org>
>                      <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>>
>                               <mailto:bioconductor at r-____project.org
>             <mailto:bioconductor at r-__project.org>
>                      <mailto:bioconductor at r-__project.org
>             <mailto:bioconductor at r-project.org>>>>>).
>
>
>                                                 Section 7 may also be of
>             use to you,
>                      as it
>                               deals with
>                                            chromosome
>                                                 anomaly detection.
>
>                                                 best wishes,
>                                                 Stephanie
>
>
>                                                 On 4/23/13 7:54 PM, Sam
>             Rose wrote:
>
>                                                     Hi Stephanie,
>
>                                                     My name is Sam Rose
>             and I am
>                      contacting
>                               you the
>                                            GWASTools package in
>                                                     Bioconductor of
>             which it says you
>                      are the
>                               maintainer.
>
>                                                     I am trying to use
>             the package to
>                      call
>                               mosaic CNVs
>                                            in my samples and
>                                                     can't seem to get it
>             to work.
>
>                                                     I'm wondering if you
>             have an
>                      example of
>                               the raw
>                                            illumina data to
>                                                     put in
>                                                     there, and maybe
>             examples of some
>                      of the
>                               things
>                                            required in the
>                                                     'ncdfAddData'
>             command (i.e.
>                      sample column,
>                                            col.nums). I have
>                                                     created the
>                                                     shell ncdf file, but
>             beyond that the
>                               headers and
>                                            data formats
>                                                     seem to be
>                                                     giving me trouble so
>             I just
>                      though I would
>                               ask.
>
>                                                     Our Illumina raw
>             data files look
>
>
>
>
>     --
>     -----
>     *Sam Rose, Stanley Center Research Associate II
>     Stanley Center for Psychiatric Research, The Broad Institute
>     7 Cambridge Center, Cambridge, MA 02142*
>     617.714.7853, srose at broadinstitute.org <mailto:srose at broadinstitute.org>
>
>
>
>
> --
> -----
> *Sam Rose, Stanley Center Research Associate II
> Stanley Center for Psychiatric Research, The Broad Institute
> 7 Cambridge Center, Cambridge, MA 02142*
> 617.714.7853, srose at broadinstitute.org <mailto:srose at broadinstitute.org>
>



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