[BioC] a question about how to use ChIPseqR

[humburg at well.ox.ac.uk]

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)
>>
>>
>
>