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]