Hi, Herve: Thanks for the suggestion. After I updated the package, It worked for the following code: 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) > Thanks again! Sabrina 2010/3/2 Hervé Pagès <hpages@fhcrc.org> > 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 installation is outdated.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@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@fhcrc.org > Phone: (206) 667-5791 > Fax: (206) 667-1319 > -- Sabrina [[alternative HTML version deleted]]