Question: getReadCountsFromBAM including bed information
0
gravatar for Pau Marc Muñoz Torres
2.3 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

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
>

 

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Pau Marc Muñoz Torres20
Answer: getReadCountsFromBAM including bed information
0
gravatar for Pau Marc Muñoz Torres
2.3 years ago by
Barcelona
Pau Marc Muñoz Torres20 wrote:

solved using  X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr)

ADD COMMENTlink written 2.3 years ago by Pau Marc Muñoz Torres20
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