[Bioc-sig-seq] [BioC] ShortRead with BAM

[James W. MacDonald]

Hi Duke,

There are two problems here. First, you have to explicitly use the 
'type' argument, as that is passed in via the '...' argument.

Second, there is a bug in readAligned() when you use type="BAM" anyway. 
Instead of dispatching the correct function, it just returns the 
function definition. I have fixed the bug in both the devel and release 
versions. The fixed release version will appear in 36 hours or so. Look 
for version 1.6.2

Best,

Jim



Duke wrote:
> On 4/28/10 10:17 AM, James W. MacDonald wrote:
>> Hi Duke,
>>
>> Still the wrong list. You want Bioc-sig-sequencing.
> 
> Thanks :D. I thought ShortRead (and other NGS packages) is in 
> BioConductor group too, but I forgot cc'ing to bioc-sig-sequencing group.
> 
>>
>> Duke wrote:
>>> Hi all,
>>>
>>> I am totally new to both R and BioConductor, so please be easy on me. 
>>> I just updated my R package to 2.11, and installed new ShortRead 
>>> package, but it seems that I am doing something wrong, and that there 
>>> is some changes from ShortRead 1.5 to 1.6 (like the command format 
>>> etc...). I tried to read a BAM file by creating a file as follow:
>>
>> You don't want the ShortRead package. You want Rsamtools, and the 
>> scanBam() function. See ?scanBam for more info.
> 
> Thanks for pointing this out. I will try Rsamtools. But readAligned does 
> have *BAM* type now. How can I use it?
> 
> D.
> 
>>
>> Best,
>>
>> Jim
>>
>>
>>>
>>> library(ShortRead)
>>> sp <- SolexaPath('/Volumes/Data/analysis/glamblia/STATs')
>>> ap <- analysisPath(sp)
>>> (aln0 <- readAligned(ap, "WB4day.bwa.def.bam", "BAM"))
>>>
>>> but running the above just gave me the content of dirPath function. 
>>> My package infos is:
>>>
>>> > sessionInfo()
>>> R version 2.11.0 (2010-04-22)
>>> x86_64-apple-darwin9.8.0
>>>
>>> locale:
>>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>>>
>>> attached base packages:
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>> [1] ShortRead_1.6.0     Rsamtools_1.0.0     lattice_0.18-5
>>> [4] Biostrings_2.16.0   GenomicRanges_1.0.1 IRanges_1.6.0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] Biobase_2.8.0 grid_2.11.0   hwriter_1.2   tools_2.11.0
>>>
>>> Anybody has any idea?
>>>
>>> Thanks,
>>>
>>> D.
>>>
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>>
> 

-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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