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@humburgwelloxacuk-5031
Last seen 10.5 years ago
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)
>>
>>
>
>