Hi,

summarizeOverlaps seems to take only BamFileList. Is there a way that it could work on a piece of a BamFile say something created via ScanBam?

input<-GRanges(seqnames = c("chr1"), ranges = IRanges(c(start),c(stop)))

range<-ScanBamParam(which=input)

binfo<-scanBam(bfile,param=range)

#coerce binfo into BamFileList?

summarizeOverlaps(features,binfolist)

if not summarizeOverlaps is there an alternative method?

The ?summarizeOverlaps man page lists all data types for the 'reads' argument:

   reads: A GRanges, GRangesList GAlignments, GAlignmentsList,
          GAlignmentPairs, BamViews or BamFileList object that
          represents the data to be counted by ‘summarizeOverlaps’.

          ‘reads’ is missing when a BamViews object is the only
          argument supplied to ‘summarizeOverlaps’.  ‘reads’ are the
          files specified in ‘bamPaths’ of the BamViews object.

Instead of reading the data in first with scanBam() you can provide a ScanBamParam to summarizeOverlaps() as the 'pram' argument. If you want to read the data in for some other reason I would suggest using the readGAlignments() family of functions. See ?readGAlignments in the GenomicAlignments package. The GAlignments or GAlignmentsList class can then be passed to summarizeOverlaps().

Valerie