Good morning
I am traying to analize some bam files using cn.mops. The scipt I am using until I try to introduce Graneges object to the getReadCountsFromBAM function. To read the bed file and convert it to Granges object i use a funtion (the code is in this post). Nevetheless i am getting the following error:
Error in exomeCopy::countBamInGRanges(bam.file = BAMFiles[i], granges = GR, :
unused argument (GR = <S4 object of class "GRanges">)
Can anyone tell me what is wrong?
Thanks
> BAMFiles <- list.files(pattern="_RG.bam$")
bed<-bed_to_granges("Genes_part.bed")
> bamDataRanges <- getReadCountsFromBAM(BAMFiles,sampleNames, refSeqNames,GR=bed)
Identified the following reference sequences: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y
Using 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y as reference.
PLEASE BE PATIENT... this might take a while. Consider using the parallel version of this function
Error in exomeCopy::countBamInGRanges(bam.file = BAMFiles[i], granges = GR, :
unused argument (GR = <S4 object of class "GRanges">)
> typeof(bed)
[1] "S4"
bed_to_granges <- function(file){
df <- read.table(file,
header=F,
stringsAsFactors=F)
if(length(df) > 6){
df <- df[,-c(7:length(df))]
}
if(length(df)<3){
stop("File has less than 3 columns")
}
header <- c('chr','start','end','id','score','strand')
names(df) <- header[1:length(names(df))]
if('strand' %in% colnames(df)){
df$strand <- gsub(pattern="[^+-]+", replacement = '*', x = df$strand)
}
if(length(df)==3){
gr <- with(df, GRanges(chr, IRanges(start, end)))
} else if (length(df)==4){
gr <- with(df, GRanges(chr, IRanges(start, end), id=id))
} else if (length(df)==5){
gr <- with(df, GRanges(chr, IRanges(start, end), id=id, score=score))
} else if (length(df)==6){
gr <- with(df, GRanges(chr, IRanges(start, end), id=id, score=score, strand=strand))
}
return(gr)
}
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 18.1
Matrix products: default
BLAS: /usr/lib/libblas/libblas.so.3.6.0
LAPACK: /usr/lib/lapack/liblapack.so.3.6.0
locale:
[1] C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Biobase_2.36.2 cn.mops_1.22.0 GenomicRanges_1.28.3
[4] GenomeInfoDb_1.12.2 IRanges_2.10.2 S4Vectors_0.14.3
[7] BiocGenerics_0.22.0
loaded via a namespace (and not attached):
[1] Rsamtools_1.28.0 Biostrings_2.44.1
[3] bitops_1.0-6 exomeCopy_1.22.0
[5] zlibbioc_1.22.0 XVector_0.16.0
[7] BiocParallel_1.10.1 RCurl_1.95-4.7
[9] compiler_3.4.1 GenomeInfoDbData_0.99.0
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