Hi,

I am facing a problem using diffBind version 1.12.3 (see sessionInfo below).

when running dba.count, I get an error

> x <- dba.count(x,minOverlap = 1,score='DBA_SCORE_READS_FOLD')
Error in pv$peaks[[i]] : subscript out of bounds

Whatever scoring method I use, the error remains the same. The error seems to be caused by the bamReads file, as using a different bam file works. However, this bam file looks completely normal when looking at in the IGV.

Any idea what might cause this kind of error ?

Thanks for your help,

Carl

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] DiffBind_1.12.3         GenomicAlignments_1.2.1 Rsamtools_1.18.2        Biostrings_2.34.1       XVector_0.6.0          
 [6] limma_3.22.5            GenomicRanges_1.18.4    GenomeInfoDb_1.2.4      IRanges_2.0.1           S4Vectors_0.4.0        
[11] BiocGenerics_0.12.1     BiocInstaller_1.16.4   

loaded via a namespace (and not attached):
 [1] amap_0.8-14        base64enc_0.1-2    BatchJobs_1.5      BBmisc_1.9         BiocParallel_1.0.3 bitops_1.0-6      
 [7] brew_1.0-6         caTools_1.17.1     checkmate_1.5.1    codetools_0.2-9    DBI_0.3.1          digest_0.6.8      
[13] edgeR_3.8.6        fail_1.2           foreach_1.4.2      gdata_2.13.3       gplots_2.16.0      grid_3.1.2        
[19] gtools_3.4.1       iterators_1.0.7    KernSmooth_2.23-14 lattice_0.20-29    RColorBrewer_1.1-2 RSQLite_1.0.0     
[25] sendmailR_1.2-1    stringr_0.6.2      tools_3.1.2        zlibbioc_1.12.0   

Hi Carl-

Before we dive too deeply into diagnosing this, can you try adding bUseSummarizeOverlaps=FALSE to the call to dba.count()?

>  x <- dba.count(x,minOverlap = 1,score='DBA_SCORE_READS_FOLD', bUseSummarizeOverlaps=FALSE)

This provides an alternative method for counting reads and will tell us if the issues is in our counting code.

Cheers-

Rory