[R] TCGA biolinks, DNA methylation

[William Dunlap]

It looks like it is not a UTF-16 text file, although it could be UTF-16
with a different byte order.
Look at it with a text editor or Excel or 'od' or 'file' (the latter are
Unix utilities) or ask the person
you got it from to see what the file contains.

Bill Dunlap
TIBCO Software
wdunlap tibco.com

On Fri, Aug 31, 2018 at 6:01 PM, Spencer Brackett <
spbrackett20 using saintjosephhs.com> wrote:

> Thank you Mr. Dunlap for the suggestion. How would this modified read.csv
> file read? This is my attempt at what you suggested, which is obviously
> errored.
>
> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=
> TRUE,fileEncoding="UTF-16")
> Warning messages:
> 1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   invalid input found on input connection 'GBM_clinical_drug.csv'
> 2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   incomplete final line found by readTableHeader on 'GBM_clinical_drug.csv'
> >  the_data<-read.csv(file="GBM_clinical_drug.csv",header=
> TRUE,sep=",",fileEncoding="UTF-16")
> Warning messages:
> 1: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   invalid input found on input connection 'GBM_clinical_drug.csv'
> 2: In read.table(file = file, header = header, sep = sep, quote = quote,  :
>   incomplete final line found by readTableHeader on 'GBM_clinical_drug.csv'
>
> Many thanks,
>
> Spencer Brackett
> >
>
>
> On Fri, Aug 31, 2018 at 11:12 AM William Dunlap <wdunlap using tibco.com> wrote:
>
>> Try adding fileEncoding="UTF-16" to your read.csv() call.  Many Windows
>> programs write UTF-16 files by default.
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>> On Thu, Aug 30, 2018 at 6:05 PM, Spencer Brackett <
>> spbrackett20 using saintjosephhs.com> wrote:
>>
>>> My apologies... the following is what I received from the correction
>>>
>>>  the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep=",")
>>> Warning messages:
>>> 1: In read.table(file = file, header = header, sep = sep, quote =
>>> quote,  :
>>>   line 3 appears to contain embedded nulls
>>> 2: In read.table(file = file, header = header, sep = sep, quote =
>>> quote,  :
>>>   line 4 appears to contain embedded nulls
>>> 3: In read.table(file = file, header = header, sep = sep, quote =
>>> quote,  :
>>>   line 5 appears to contain embedded nulls
>>> 4: In scan(file = file, what = what, sep = sep, quote = quote, dec =
>>> dec,  :
>>>   embedded nul(s) found in input
>>> >
>>>
>>>
>>> On Thu, Aug 30, 2018 at 8:57 PM Patrick Barry <pdbarry using alaska.edu>
>>> wrote:
>>>
>>> > You still haven't fixed the first thing both Sarah and I pointed out.
>>> You
>>> > are lacking an = between sep and ","
>>> >
>>> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",")
>>> >
>>> > should be
>>> >
>>> > the_data <- read.csv(file = "GBM_clinical_drug.csv", header = TRUE,
>>> *sep
>>> > = ","*)
>>> >
>>> > as Sarah pointed out, you should use spaces to help make these errors
>>> more
>>> > obvious.
>>> >
>>> > On Thu, Aug 30, 2018 at 4:53 PM, Spencer Brackett <
>>> > spbrackett20 using saintjosephhs.com> wrote:
>>> >
>>> >> Hello again,
>>> >>
>>> >> My apologies for the delayed response... computer troubles. In
>>> reference
>>> >> to
>>> >> Ms. Goslee's and Mr. Barry's query, the following is the error code
>>> >> received after I inputted my R command
>>> >>
>>> >>  the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",")
>>> >> Error: unexpected string constant in
>>> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=TRUE,sep",""
>>> >>
>>> >> Given this, should I proceed with implementing the path<getwd()
>>> ,since I
>>> >> am, as he suggested trying to set the variable *path* to my working
>>> >> directory with path<-"."
>>> >>
>>> >> Mr. Mittal also recommended importing with r studio, which I shall
>>> try in
>>> >> the meantime.
>>> >>
>>> >> Many thanks,
>>> >>
>>> >> Spencer Brackett
>>> >>
>>> >>
>>> >> On Wed, Aug 29, 2018 at 10:14 PM Amit Mittal <
>>> prof.amit.mittal using gmail.com>
>>> >> wrote:
>>> >>
>>> >> > Use r studio and import from the menu. Read_csv has changed
>>> >> >
>>> >> > Also you can see any format problems
>>> >> >
>>> >> > On Thu, 30 Aug 2018 3:36 am Spencer Brackett, <
>>> >> > spbrackett20 using saintjosephhs.com> wrote:
>>> >> >
>>> >> >> Good evening R users,
>>> >> >>
>>> >> >>   I am attempting to carry out DNA methylation analysis on two
>>> separate
>>> >> >> CSV
>>> >> >> files (LGG and GBM), which I have downloaded onto my R console. To
>>> set
>>> >> the
>>> >> >> path<-"." to be indicative of one or both of the csv files, I
>>> utilized
>>> >> the
>>> >> >> following functions and received the errors shown. How do I set the
>>> >> "." so
>>> >> >> that I can begin analysis on my files?
>>> >> >>
>>> >> >> > the_data <-read.csv(file="LGG_clinical_
>>> drug.csv",header=T,sep",")
>>> >> >> Error: unexpected string constant in "the_data
>>> >> >> <-read.csv(file="LGG_clinical_drug.csv",header=T,sep",""
>>> >> >> > the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",")
>>> >> >> Error: unexpected string constant in
>>> >> >> "the_data<-read.csv(file="GBM_clinical_drug.csv",header=T,sep",""
>>> >> >>
>>> >> >> This is the preliminary portion of the analysis I am trying to run,
>>> >> which
>>> >> >> I
>>> >> >> am referring to:
>>> >> >>
>>> >> >> 1 library(TCGAbiolinks)
>>> >> >> 2
>>> >> >> 3 # Download the DNA methylation data: HumanMethylation450 LGG and
>>> GBM.
>>> >> >> 4 path <– "."
>>> >> >> 5
>>> >> >> 6 query.met <– TCGAquery(tumor = c("LGG","GBM"),"
>>> HumanMethylation450",
>>> >> >> level = 3)
>>> >> >> 7 TCGAdownload(query.met, path = path )
>>> >> >> 8 met <– TCGAprepare(query = query.met,dir = path,
>>> >> >> 9                      add.subtype = TRUE, add.clinical = TRUE,
>>> >> >> 10                    summarizedExperiment = TRUE,
>>> >> >> 11                      save = TRUE, filename = "lgg_gbm_met.rda")
>>> >> >> 12
>>> >> >> 13 # Download the expression data: IlluminaHiSeq_RNASeqV2 LGG and
>>> GBM.
>>> >> >> 14 query.exp <– TCGAquery(tumor = c("lgg","gbm"), platform =
>>> >> >> "IlluminaHiSeq_
>>> >> >> RNASeqV2",level = 3)
>>> >> >> 15
>>> >> >> 16 TCGAdownload(query.exp,path = path, type =
>>> "rsem.genes.normalized_
>>> >> >> results")
>>> >> >> 17
>>> >> >> 18 exp <– TCGAprepare(query = query.exp, dir = path,
>>> >> >> 19                    summarizedExperiment = TRUE,
>>> >> >> 20                      add.subtype = TRUE, add.clinical = TRUE,
>>> >> >> 21                    type = "rsem.genes.normalized_results",
>>> >> >> 22                      save = T,filename = "lgg_gbm_exp.rda")
>>> >> >>
>>> >> >> Many thanks,
>>> >> >>
>>> >> >> Spencer Brackett
>>> >> >>
>>> >> >>         [[alternative HTML version deleted]]
>>> >> >>
>>> >> >> ______________________________________________
>>> >> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> >> >> https://stat.ethz.ch/mailman/listinfo/r-help
>>> >> >> PLEASE do read the posting guide
>>> >> >> http://www.R-project.org/posting-guide.html
>>> >> >> and provide commented, minimal, self-contained, reproducible code.
>>> >> >>
>>> >> >
>>> >>
>>> >>         [[alternative HTML version deleted]]
>>> >>
>>> >> ______________________________________________
>>> >> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> >> https://stat.ethz.ch/mailman/listinfo/r-help
>>> >> PLEASE do read the posting guide
>>> >> http://www.R-project.org/posting-guide.html
>>> >> and provide commented, minimal, self-contained, reproducible code.
>>> >>
>>> >
>>> >
>>>
>>>         [[alternative HTML version deleted]]
>>>
>>> ______________________________________________
>>> R-help using r-project.org mailing list -- To UNSUBSCRIBE and more, see
>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>> PLEASE do read the posting guide http://www.R-project.org/
>>> posting-guide.html
>>> and provide commented, minimal, self-contained, reproducible code.
>>>
>>
>>

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