plotSeqLogo: Plot seqlogo for poly(A) signals.

In BMILAB/movAPA: movAPA: Modeling and Visualization of Dynamics of Alternative PolyAdenylation

Plot seqlogo for poly(A) signals.

Description

plotSeqLogo plots seqlogo for poly(A) signals by utilizing the motifStack package.

Usage

plotSeqLogo(pas)

Arguments

pas	a vector of k-grams, normally from annotateByPAS().

Value

A plot of seqlogo.

See Also

Other APA signal functions: annotateByPAS(), faFromPACds(), getVarGrams(), kcount(), plotATCGforFAfile()

Examples

data(PACds)
library("BSgenome.Oryza.ENSEMBL.IRGSP1")
bsgenome <- BSgenome.Oryza.ENSEMBL.IRGSP1
PACdsPAS=annotateByPAS(PACds, bsgenome, grams='V1',
                       from=-50, to=-1, label=NULL)
pas=PACdsPAS@anno$V1_gram[!is.na(PACdsPAS@anno$V1_gram)]
plotSeqLogo(pas)

BMILAB/movAPA documentation built on Jan. 3, 2024, 11:09 p.m.