[BioC] dba.counts error

[Ravi Karra]

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