seqlogo {spliceSites}R Documentation

seqlogo: Plotting sequence logo for 'cdRanges' and 'dnaGapSites' objects.

Description

The function produces a sequence logo plot based on the contained sequences.

Usage

seqlogo(x,strand="+",useStrand=TRUE,...)

Arguments

x

cdRanges or dnaGapSites Object.

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 useStrand=FALSE the plot is made up from all contained sequences.

...

(Currently unused)

Details

The function fails with an error message when the dataset does not contain any records with the given strand (except useStrand=FALSE).

Value

None

Author(s)

Wolfgang Kaisers

Examples

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)
[Package spliceSites version 1.28.0 Index]