On 11/18/2010 10:11 AM, Kunbin Qu wrote:
> Hi, all:
>
> I was trying to use positionFilter from the ShortRead, and
> encountered the following error. Could anybody help me? Thanks.
>
Hi Kunbin --
positionFilter requires that the reads are aligned to a genome, but
fastq files do not have this information. Martin
> -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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--
Computational Biology
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