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.

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"

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

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