Question

Error using 'scanForHeterozygotes' function in AllelicImbalance package

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JK ▴ 10

@jk-6972

Last seen 8.7 years ago

United States

Hi,

I generated BAM files using the STAR aligner. I am having some issues working with these BAM files in AllelicImbalance:

I would appreciate some help with the issue.

Best,

Jozsef

> pathToFiles='h:/AGP_hg19_filtered_fastq_bam'
> searchArea<-GRanges(seqnames = c("chr11"),ranges = IRanges(35228000, 35230000))
> reads <- impBamGAL(pathToFiles,searchArea,verbose=T)
Reading bam file 1 with filename AGP001_Aligned.sortedByCoord.out.bam 
stored AGP001_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 2 with filename AGP002_Aligned.sortedByCoord.out.bam 
stored AGP002_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 3 with filename AGP003_Aligned.sortedByCoord.out.bam 
stored AGP003_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 4 with filename AGP004_Aligned.sortedByCoord.out.bam 
stored AGP004_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 5 with filename AGP006_Aligned.sortedByCoord.out.bam 
stored AGP006_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 6 with filename AGP007_Aligned.sortedByCoord.out.bam 
stored AGP007_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 7 with filename AGP009_Aligned.sortedByCoord.out.bam 
stored AGP009_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 8 with filename AGP012_Aligned.sortedByCoord.out.bam 
stored AGP012_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 9 with filename AGP013_Aligned.sortedByCoord.out.bam 
stored AGP013_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 10 with filename AGP022_Aligned.sortedByCoord.out.bam 
stored AGP022_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 11 with filename AGP025_Aligned.sortedByCoord.out.bam 
stored AGP025_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 12 with filename AGP027_Aligned.sortedByCoord.out.bam 
stored AGP027_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 13 with filename AGP029_Aligned.sortedByCoord.out.bam 
stored AGP029_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 14 with filename AGP040_Aligned.sortedByCoord.out.bam 
stored AGP040_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 15 with filename AGP041_Aligned.sortedByCoord.out.bam 
stored AGP041_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 16 with filename AGP044_Aligned.sortedByCoord.out.bam 
stored AGP044_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 17 with filename AGP046_Aligned.sortedByCoord.out.bam 
stored AGP046_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 18 with filename AGP061_Aligned.sortedByCoord.out.bam 
stored AGP061_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 19 with filename H1_Aligned.sortedByCoord.out.bam 
stored H1_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 20 with filename H10_Aligned.sortedByCoord.out.bam 
stored H10_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 21 with filename H11_Aligned.sortedByCoord.out.bam 
stored H11_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 22 with filename H12_Aligned.sortedByCoord.out.bam 
stored H12_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 23 with filename H13_Aligned.sortedByCoord.out.bam 
stored H13_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 24 with filename H14_Aligned.sortedByCoord.out.bam 
stored H14_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 25 with filename H15_Aligned.sortedByCoord.out.bam 
stored H15_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 26 with filename H2_Aligned.sortedByCoord.out.bam 
stored H2_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 27 with filename H3_Aligned.sortedByCoord.out.bam 
stored H3_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 28 with filename H4_Aligned.sortedByCoord.out.bam 
stored H4_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 29 with filename H5_Aligned.sortedByCoord.out.bam 
stored H5_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 30 with filename H6_Aligned.sortedByCoord.out.bam 
stored H6_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 31 with filename H7_Aligned.sortedByCoord.out.bam 
stored H7_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 32 with filename H8_Aligned.sortedByCoord.out.bam 
stored H8_Aligned.sortedByCoord.out.bam in BamGAL 
Reading bam file 33 with filename H9_Aligned.sortedByCoord.out.bam 
stored H9_Aligned.sortedByCoord.out.bam in BamGAL 
> heterozygotePositions <- scanForHeterozygotes(reads, maxReads=1e+07, verbose=TRUE)
Investigating chromosome chr11 
Investigating sample 1 out of 33 
Error in new[start[i]:(start[i] + length(toKeep[[i]]) - 1), i] <- charList[[i]][toKeep[[i]]] : 
  number of items to replace is not a multiple of replacement length
> searchArea<-GRanges(seqnames = c("11"),ranges = IRanges(35228000, 35230000))
> reads <- impBamGAL(pathToFiles,searchArea,verbose=T)
Error in impBamGAL(pathToFiles, searchArea, verbose = T) : 
  The following seq name(s) not found in the bam files: 11
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

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

other attached packages:
 [1] org.Hs.eg.db_3.0.0      RSQLite_1.0.0           DBI_0.3.1               AnnotationDbi_1.28.1    Biobase_2.26.0         
 [6] AllelicImbalance_1.4.0  GenomicAlignments_1.2.2 Rsamtools_1.18.3        Biostrings_2.34.1       XVector_0.6.0          
[11] GenomicRanges_1.18.4    GenomeInfoDb_1.2.4      IRanges_2.0.1           S4Vectors_0.4.0         BiocGenerics_0.12.1    

loaded via a namespace (and not attached):
 [1] acepack_1.3-3.3          base64enc_0.1-2          BatchJobs_1.5            BBmisc_1.8              
 [5] BiocParallel_1.0.3       biomaRt_2.22.0           biovizBase_1.14.1        bitops_1.0-6            
 [9] brew_1.0-6               BSgenome_1.34.1          checkmate_1.5.0          cluster_1.15.3          
[13] codetools_0.2-9          colorspace_1.2-4         dichromat_2.0-0          digest_0.6.4            
[17] fail_1.2                 foreach_1.4.2            foreign_0.8-61           Formula_1.1-2           
[21] GenomicFeatures_1.18.3   Gviz_1.10.10             Hmisc_3.14-6             iterators_1.0.7         
[25] lattice_0.20-29          latticeExtra_0.6-26      matrixStats_0.10.3       munsell_0.4.2           
[29] nnet_7.3-8               plyr_1.8.1               R.methodsS3_1.6.1        RColorBrewer_1.0-5      
[33] Rcpp_0.11.3              RCurl_1.95-4.4           rpart_4.1-8              rtracklayer_1.26.2      
[37] scales_0.2.4             sendmailR_1.2-1          splines_3.1.2            stringr_0.6.2           
[41] survival_2.37-7          tools_3.1.2              VariantAnnotation_1.12.9 XML_3.98-1.1            
[45] zlibbioc_1.12.0

allelicimbalance • 1.4k views

ADD COMMENT • link updated 8.9 years ago by Jesper Robert Gadin ▴ 20 • written 9.1 years ago by JK ▴ 10

score 0 · Answer 1 · 2015-06-01

Hello,

There are two errors here,

1)

Error in new[start[i]:(start[i] + length(toKeep[[i]]) - 1), i] <- charList[[i]][toKeep[[i]]] :
  number of items to replace is not a multiple of replacement length

Has been solved, see here (https://github.com/pappewaio/AllelicImbalance/issues/3)

2)

> searchArea<-GRanges(seqnames = c("11"),ranges = IRanges(35228000, 35230000)) > reads <- impBamGAL(pathToFiles,searchArea,verbose=T) Error in impBamGAL(pathToFiles, searchArea, verbose = T) : The following seq name(s) not found in the bam files: 11

Based on that your code,

searchArea<-GRanges(seqnames = c("chr11"),ranges = IRanges(35228000, 35230000))

works, there is no seqlevel "11" in the bam files, and so it generate an error. Use "chr11" and it will work.

Jesper