[Bioc-sig-seq] Coverage for RangeList?
Jane Landolin
landolin at gmail.com
Tue Apr 20 19:12:27 CEST 2010
Ah, ok, thanks for all the comments. My version of IRanges is not up
to date and doesn't have the width parameter. I'm upgrading and will
let you know if I still have issues.
Right now, I am organizing the chromosomes using the "splitter"
parameter in RangedData(), and get an "unused arguments" error when I
call coverage() with a "width" parameter:
ir<-IRanges(start=as.numeric(rrna_k[,"start"]),end=as.numeric(rrna_k[,"stop"]))
seq<-rrna_k[,"seq"]
strand<-rrna_k[,"strand"]
chr_length<-rrna_lengths[rownames(rrna_k)]
rrna_k_rd<-RangedData(ir,seq,strand,chr_length,splitter=rrna_k[,"chr"])
> lapply(ranges(rrna_k_rd),coverage,width=rrna_lengths)
Error in .local(x, start, end, ...) :
unused argument(s) (width = c(135, 135,1130,1140,
Jane
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