[BioC] dba.counts error

[Ravi Karra]

Thanks Rory, 
I missed that requirement. 
Works perfectly now!
Ravi

On Jun 10, 2014, at 9:51 AM, Rory Stark <Rory.Stark at cruk.cam.ac.uk> wrote:

> 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  
>