[BioC] getSeq error with multiple inqueries, BSgenome

[Hervé Pagès]

Hi Sabrina,

sabrina s wrote:
> Hi, All:
> I am trying to use getSeq to retrieve sequences for a list of coordinates I
> have which involves many chromosomes. this is a continuous discussion that I
> had from yesterday. But I think I need to change the subject title for this
> particular question.

Not sure changing the subject is particularly useful...

> 
> I already created a long list of coordinates  by the following code:
> testIranges<- IRanges(start=currCoorList $starts,
>         end=currCoorLis$ends)
> 
>    testTrack<-GenomicData(
> testIranges,chrom=currCoorList$chr,
>         strand=currCoorList$strand,genome="mm9")
> 
> According to Michael's suggestion, I used the following code to retrieve the
> sequence:
> 
> myseq<-getSeq(Mmusculus, testTrack)
> 
> and I got the error:
>  Error in IRanges:::.normargSEW(start, "start") :
>   'start' must be a vector of integers
> 
> So I decided to troubleshoot it using simple examples.
> 
> I used the following code:
>  myseqs <- data.frame(chr=  "chr4",   start= 101390513,    end= 101390523)
> getSeq(Mmusculus,myseqs$chr,start=myseqs$start, end=myseqs$end)
> 
> IT WORKED. BUT when I used the following:
> 
> myseqs <- data.frame(chr= c("chr4","chr7"),
>      start=c(101390513,137720998),
>      end=c(101390523,137721010)  )
> 
> getSeq(Mmusculus,myseqs$chr,start=myseqs$start, end=myseqs$end)
> 
> It gave me an error:
> Error in reverseComplement(DNAStringSet(seqs[ii])) :
>   could not find function "copy"

This works for me. It's very likely that you get this because your
installation is outdated. Please try to update it first (as explained
in my previous email) and let us know if that solves the problem.

Thanks,
H.

> 
> My session info is :
> R version 2.10.0 (2009-10-26)
> i386-pc-mingw32
> 
> locale:
> [1] LC_COLLATE=English_United States.1252
> [2] LC_CTYPE=English_United States.1252
> [3] LC_MONETARY=English_United States.1252
> [4] LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] BSgenome.Mmusculus.UCSC.mm9_1.3.16 BSgenome_1.14.2
> [3] Biostrings_2.14.5                  rtracklayer_1.6.0
> [5] RCurl_1.3-1                        bitops_1.0-4.1
> [7] IRanges_1.4.10
> 
> loaded via a namespace (and not attached):
> [1] Biobase_2.6.0 tools_2.10.0  XML_2.6-0
> 
> Can anyone help? Thanks!
> 
> Sabrina
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M2-B876
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319