Hi,

I would appreciate some help with the error below. I am trying to process Bowtie2-aligened and subsequently Rsamtools sorted and indexed bam files with the package AllelicImbalance according to the manual on the Bioconductor page. I am getting the error below:

> searchArea <- GRanges(seqnames = c("chr17"),ranges = IRanges(79478000,79478361))
> reads <- impBamGAL('/site/ne/home/karjo01/AGP001_bowtie2',searchArea,verbose=FALSE)
> heterozygotePositions <- scanForHeterozygotes(reads,verbose=FALSE)

> countList <- getAlleleCounts(reads, heterozygotePositions, verbose=FALSE)
Error in `colnames<-`(`*tmp*`, value = c("A", "C", "G", "T")) :
  attempt to set 'colnames' on an object with less than two dimensions

> 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              
 [3] 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   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] AllelicImbalance_1.4.0  GenomicAlignments_1.2.1 Rsamtools_1.18.2       
 [4] Biostrings_2.34.1       XVector_0.6.0           GenomicRanges_1.18.4   
 [7] GenomeInfoDb_1.2.4      IRanges_2.0.1           S4Vectors_0.4.0        
[10] BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          AnnotationDbi_1.28.1     base64enc_0.1-2         
 [4] BatchJobs_1.5            BBmisc_1.8               Biobase_2.26.0          
 [7] BiocParallel_1.0.0       biomaRt_2.22.0           biovizBase_1.14.1       
[10] bitops_1.0-6             brew_1.0-6               BSgenome_1.34.1         
[13] checkmate_1.5.1          cluster_1.15.3           codetools_0.2-10        
[16] colorspace_1.2-4         DBI_0.3.1                dichromat_2.0-0         
[19] digest_0.6.8             fail_1.2                 foreach_1.4.2           
[22] foreign_0.8-62           Formula_1.1-2            GenomicFeatures_1.18.3  
[25] Gviz_1.10.5              Hmisc_3.14-6             iterators_1.0.7         
[28] lattice_0.20-29          latticeExtra_0.6-26      matrixStats_0.12.2      
[31] munsell_0.4.2            nnet_7.3-8               plyr_1.8.1              
[34] RColorBrewer_1.1-2       Rcpp_0.11.3              RCurl_1.95-4.5          
[37] R.methodsS3_1.6.1        rpart_4.1-8              RSQLite_1.0.0           
[40] rtracklayer_1.26.2       scales_0.2.4             sendmailR_1.2-1         
[43] splines_3.1.2            stringr_0.6.2            survival_2.37-7         
[46] tools_3.1.2              VariantAnnotation_1.12.8 XML_3.98-1.1            
[49] zlibbioc_1.12.0        

Hi,

Have you tried contacting the author directly? (j.r.gadin@gmail.com)

The error says that inside getAlleleCounts(), the code expects a matrix but is getting a one dimensional object (vector) instead. Have you confirmed the GRanges output from scanForHeterozygotes() is not empty? You could try debugging,

debug(getAlleleCounts)
countList <- getAlleleCounts(reads, heterozygotePositions, verbose=FALSE)

then step through the code with 'n'. See ?debug.

Valerie