DNAmotifAlignment: align DNA motifs

Description Usage Arguments Value Examples

View source: R/DNAmotifAlignment.R

Description

align DNA motifs for plotting motifs stack

Usage

1
2
DNAmotifAlignment(pfms, threshold=0.4, minimalConsensus=0, 
                  rcpostfix="(RC)", revcomp=rep(TRUE, length(pfms)))

Arguments

pfms

a list of position frequency matrices, pfms must be a list of class pfm or psam

threshold

information content cutoff threshold for useful postions

minimalConsensus

minimal length of consensus for alignment

rcpostfix

the postfix for reverse complements

revcomp

a logical vector to indicates whether the reverse complemet should be involved into alignment

Value

a list of aligned motifs

Examples

1
2
3
pcms<-readPCM(file.path(find.package("motifStack"), "extdata"),"pcm$")
motifs<-lapply(pcms,pcm2pfm)
motifs<-DNAmotifAlignment(motifs)

motifStack documentation built on July 24, 2018, 2 a.m.