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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