as.data.frame: Coerce to a Data Frame

In alyst/MotIV: Motif Identification and Validation

Description

This function coerces a MotIV object into a data frame.

Usage

## S4 method for signature 'motiv'
as.data.frame(x)

Arguments

x	An object of class motiv.

Details

'as.data.frame' returns a data frame.

This object regroups all the TF identified by MotIV with the corresponding evalue and alignments.

Value

A data.frame object.

Author(s)

Eloi Mercier <[e-mail]>

See Also

data.frame , viewAlignments

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)
foxa1.analysis.jaspar.df = as.data.frame(foxa1.analysis.jaspar)
head(foxa1.analysis.jaspar.df)

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