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) -- shan gao Room 231(Dr.Fei lab) Boyce Thompson Institute Cornell University Tower Road, Ithaca, NY 14853-1801 Office phone: 1-607-254-1267(day) Official email:sg839 at cornell.edu Facebook:http://www.facebook.com/profile.php?id=100001986532253

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) > >