Apologies for the late reply. There is indeed a bug in the method for AlignedRead objects. This should now be fixed in the development version. I will also patch the release after some additional testing. Thanks for reporting the issue. Please let me know if you encounter any other issues. Cheers, Peter > cc'ing Peter (package author) in case he hasn't seen this message. > > Valerie > > > On 12/11/2011 01:31 PM, wang peter wrote: >> hello all >> >> i think the strandPileup function support both of data.frame and >> readAligned object >> as import data >> so that is the coding >> >> library(ShortRead) >> library(ChIPseqR) >> bamfile<- "nuclosome_MG.bam" >> aln1<- readAligned(bamfile, type="BAM") >> counts<- strandPileup(aln1, chrLen=2e6, extend=1, coords="leftmost", >> plot=FALSE) >> Error in is.null(arg) : 'arg' is missing >> >> >> >>> sessionInfo() >> R version 2.13.2 (2011-09-30) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> > >