Print Motifs Alignments

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Description

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

Usage

1

Arguments

x

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

Details

This function shows the alignements for each motif.

Author(s)

Eloi Mercier <emercier@chibi.ubc.ca>

See Also

as.data.frame

Examples

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#####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 )