seqlogo {spliceSites} | R Documentation |
The function produces a sequence logo plot based on the contained sequences.
seqlogo(x,strand="+",useStrand=TRUE,...)
x |
|
strand |
Character. Determines the subset for which the seqlogo is plotted. This option is only used when useStrand is given as 'TRUE'. |
useStrand |
Logical. Determines whether the given strand information is used. For |
... |
(Currently unused) |
The function fails with an error message when the dataset does not contain any records with the given strand (except useStrand=FALSE).
None
Wolfgang Kaisers
bam<-system.file("extdata","rna_fem.bam",package="spliceSites") reader<-bamReader(bam,idx=TRUE) ga<-alignGapList(reader) bamClose(reader) lj<-lJunc(ga,featlen=6,gaplen=6,strand='+') dnafile<-system.file("extdata","dna_small.RData",package="spliceSites") load(dnafile) ljd<-dnaRanges(lj,dna_small) seqlogo(ljd)