[Bioc-sig-seq] positionFilter in ShortRead

Martin Morgan mtmorgan at fhcrc.org
Thu Nov 18 20:49:06 CET 2010


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"
>>
> 
> 
> ______________________________________________________________________
> The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to postmaster at genomichealth.com and delete this message, along with any attachments, from your computer.
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioc-sig-sequencing mailing list
> Bioc-sig-sequencing at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing


-- 
Computational Biology
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109

Location: M1-B861
Telephone: 206 667-2793



More information about the Bioc-sig-sequencing mailing list