Hi, all:
I was trying to use positionFilter from the ShortRead, and encountered the
following error. Could anybody help me? Thanks.
-Kunbin
library(ShortRead)
FILE<-list.files("../RAW")
f<-list()
pf<-positionFilter(min=1L, max=65L)
for(i in FILE){
f<-readFastq("../RAW", pattern=i, filter=pf, quality="FastqQuality")
}
Error in function (classes, fdef, mtable) :
unable to find an inherited method for function "position", for signature
"ShortReadQ"
Error in srq[filter(srq)] :
error in evaluating the argument 'i' in selecting a method for function '['
> sessionInfo()
R version 2.11.0 (2010-04-22)
x86_64-unknown-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_1.6.2 Rsamtools_1.0.1 lattice_0.19-11
[4] Biostrings_2.16.7 GenomicRanges_1.0.1 IRanges_1.6.8
loaded via a namespace (and not attached):
[1] Biobase_2.8.0 grid_2.11.0 hwriter_1.2
> pf
class: SRFilter
name: PositionFilter
use srFilter(object) to see filter
> i
[1] "AL2-68_GHS1.ITstd.0.25x_GHI.fastq"
>
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