Hi,
I have been using the ShortRead package with my sequencing data. It has been
making my life a lot easier.
One thing I noticed that the logic in the uniqueFilter function seems to be
problematic.
The original function is:
function (withSread = TRUE, .name = "UniqueFilter")
{
.check_type_and_length(withSread, "logical", 1)
srFilter(function(x) {
if (withSread)
!srduplicated(x)
else {
!(duplicated(position(x)) & duplicated(strand(x)) &
duplicated(chromosome(x)))
}
}, name = .name)
}
If withSread = FALSE, the else part seems to filter out lots of reads I
would like to keep.
My dumb solution is to have this change:
!(duplicated(paste(position(x), strand(x), chromosome(x),sep=";")))
I may have misused the function though.
> sessionInfo()
R version 2.10.0 (2009-10-26)
x86_64-redhat-linux-gnu
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ShortRead_1.4.0 lattice_0.17-26 BSgenome_1.14.2 Biostrings_2.14.8
[5] IRanges_1.4.9
loaded via a namespace (and not attached):
[1] Biobase_2.6.1 grid_2.10.0 hwriter_1.1 tools_2.10.0
>
Thanks,
Jason
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