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
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