Filtering Bam file based on specific regions using Rsamtools

Question

[laraib85]

I am kind of new to R and am trying to get multiple regions from my bam file and I need to write these back to a bam file using the Rsamtools library. I am trying to do it this way:

myGR <- GRanges(seqnames=c("chrIII","chrXII","chrIV"),ranges=IRanges(start=c(50838,660716,806621),end=c(52340,662833,807748)) )
myparams1<- ScanBamParam(which=myGR)
filterBam("accepted_hits.sorted.bam", "accepted_hits.specific", indexDestination=FALSE, myparams1)

but the filterBam command gives an error:

Error in as.character.default(x) :
  no method for coercing this S4 class to a vector

Any ideas how to fix this?

Answer 1

[Martin Morgan]

The param argument to filterBam comes after the ... in the argument list, so needs to be named, something like

filterBam("accepted_hits.sorted.bam", "accepted_hits.specific",
    indexDestination=FALSE, param=myparams1)