[BioC] dba.counts error

[Rory Stark]

Hi Ravi-

It looks like your sample sheet is missing the "bamReads" column, which
tells DiffBind where the bam files are that contain the aligned reads, so
dba.count doesn't know where to look for the reads to count!

Cheers-
Rory

On 10/06/2014 14:35, "Ravi Karra" <ravi.karra at gmail.com> wrote:

>Hi, 
>
>I am trying to use DiffBind to analyze my ChIP-Seq data.  I used MACS2 as
>my peak caller and to adjust for input.  I am able to use dba to load in
>the data and to generate a correlation heatmap using the MACS scores.
>
>However, I am unable to calculate a binding matrix based on affinity
>scores.  When I use dba.count (), I get the follow error message:
>
>"Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed"
>
>I am not really sure where the error is coming from and appreciate any
>help to troubleshoot.
>
>Thanks in advance,
>Ravi
>
>Code, traceback, and sessionInfo:
>
>> library (DiffBind)
>> 
>> samples = read.csv ("~/Desktop/Data/Acetyl_sampleSheet.csv", header = T)
>Warning message:
>In read.table(file = file, header = header, sep = sep, quote = quote,  :
>  incomplete final line found by readTableHeader on
>'~/Desktop/Data/Acetyl_sampleSheet.csv'
>> samples
>  SampleID Factor Condition Replicate
>1    Ac_A1  K27Ac         A         1
>2    Ac_A2  K27Ac         A         2
>3    Ac_C1  K27Ac         C         1
>4    Ac_C2  K27Ac         C         2
>                                                    Peaks
>1 /Users/rk16/Desktop/Data/Ac_A1_input_adjusted_peaks.xls
>2 /Users/rk16/Desktop/Data/Ac_A2_input_adjusted_peaks.xls
>3 /Users/rk16/Desktop/Data/Ac_C1_input_adjusted_peaks.xls
>4 /Users/rk16/Desktop/Data/Ac_C2_input_adjusted_peaks.xls
>  PeakCaller
>1       macs
>2       macs
>3       macs
>4       macs
>>  Ac = dba(sampleSheet = samples)
>Ac_A1  K27Ac A  1 macs
>Ac_A2  K27Ac A  2 macs
>Ac_C1  K27Ac C  1 macs
>Ac_C2  K27Ac C  2 macs
>>  Ac = dba.count(Ac, minOverlap=2)
>Error in if (res[i] == -1) { : missing value where TRUE/FALSE needed
>>  traceback ()
>3: pv.checkExists(todo)
>2: pv.counts(DBA, peaks = peaks, minOverlap = minOverlap, defaultScore =
>score, 
>       bLog = bLog, insertLength = fragmentSize, bOnlyCounts = T,
>       bCalledMasks = TRUE, minMaxval = filter, bParallel = bParallel,
>       bUseLast = bUseLast, bWithoutDupes = bRemoveDuplicates,
>bScaleControl = bScaleControl,
>       filterFun = filterFun, bLowMem = bUseSummarizeOverlaps, readFormat
>= readFormat, 
>       summits = summits, minMappingQuality = mapQCth)
>1: dba.count(Ac, minOverlap = 2)
>>  sessionInfo ()
>R version 3.1.0 (2014-04-10)
>Platform: x86_64-apple-darwin10.8.0 (64-bit)
>
>locale:
>[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
>attached base packages:
>[1] parallel  stats     graphics  grDevices utils     datasets
>[7] methods   base
>
>other attached packages:
> [1] DiffBind_1.10.1         GenomicAlignments_1.0.1
> [3] BSgenome_1.32.0         Rsamtools_1.16.0
> [5] Biostrings_2.32.0       XVector_0.4.0
> [7] limma_3.20.4            GenomicRanges_1.16.3
> [9] GenomeInfoDb_1.0.2      IRanges_1.22.8
>[11] BiocGenerics_0.10.0
>
>loaded via a namespace (and not attached):
> [1] amap_0.8-12        BatchJobs_1.2      BBmisc_1.6
> [4] BiocParallel_0.6.1 bitops_1.0-6       brew_1.0-6
> [7] caTools_1.17       codetools_0.2-8    DBI_0.2-7
>[10] digest_0.6.4       edgeR_3.6.2        fail_1.2
>[13] foreach_1.4.2      gdata_2.13.3       gplots_2.13.0
>[16] grid_3.1.0         gtools_3.4.1       iterators_1.0.7
>[19] KernSmooth_2.23-12 lattice_0.20-29    plyr_1.8.1
>[22] RColorBrewer_1.0-5 Rcpp_0.11.1        RSQLite_0.11.4
>[25] sendmailR_1.1-2    stats4_3.1.0       stringr_0.6.2
>[28] tools_3.1.0        zlibbioc_1.10.0