viewAlignment: Print Motifs Alignments

In alyst/MotIV: Motif Identification and Validation

Description

This function return a list of the alignments of a motiv object for each motif.

Usage

  viewAlignments(x)

Arguments

x	An object of class motiv (usualy provied by motifMatch).

Details

This function shows the alignements for each motif.

Author(s)

Eloi Mercier <[e-mail]>

See Also

as.data.frame

Examples

#####Database and Scores#####
path <- system.file(package="MotIV")
jaspar <- readPWMfile(paste(path,"/extdata/jaspar2010.txt",sep=""))
jaspar.scores <- readDBScores(paste(path,"/extdata/jaspar2010_PCC_SWU.scores",sep=""))

#####Input#####
data(FOXA1_rGADEM)
motifs <- getPWM(gadem)
motifs.trimed <- lapply(motifs,trimPWMedge, threshold=1)

#####Analysis#####
foxa1.analysis.jaspar <- motifMatch(inputPWM=motifs,align="SWU",cc="PCC",database=jaspar,DBscores=jaspar.scores,top=5)
summary(foxa1.analysis.jaspar )
viewAlignments(foxa1.analysis.jaspar )

alyst/MotIV documentation built on May 12, 2019, 2:33 a.m.