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

[Duke]

Hi Jim,

On 4/28/10 1:23 PM, James W. MacDonald wrote:
> Hi Duke,
>
> There are two problems here. First, you have to explicitly use the 
> 'type' argument, as that is passed in via the '...' argument.

Yes, I found out that I used the wrong argument as you mentioned.

>
> 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

This is great! Finally now I know why no matter what arguments I used, 
readAligned always returns the function. Thanks for letting me know this.

Thanks,

D.

>
> 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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>>>
>>
>