compareBedFiless2UserProvidedRegions: Compare a set of bed files to a user provided regions set

In ManchesterBioinference/Motif2Site: Detect binding sites from motifs and ChIP-seq experiments, and compare binding sites across conditions

Description

This function gets user provided bedfiles and compare them with a user provided region.

It returns this comparison to given user binding regions in terms of precision/recall.

Usage

compareBedFiless2UserProvidedRegions(bedfiles, motifnames, givenRegion)

Arguments

bedfiles	a vector of bed files
motifnames	a vector of the names related to bed files
givenRegion	granges of user provided binding regions

Value

A dataframe which includes precision recall values for each bed file

See Also

compareMotifs2UserProvidedRegions

Examples

yeastExampleFile=system.file("extdata", "YeastSampleMotif.bed",
                              package="Motif2Site")
YeastRegionsChIPseq <- Bed2Granges(yeastExampleFile)
bed1 <- system.file("extdata", "YeastBedFile1.bed", package="Motif2Site")
bed2 <- system.file("extdata", "YeastBedFile2.bed", package="Motif2Site")
BedFilesVector <- c(bed1, bed2)
SequenceComparison <- compareBedFiless2UserProvidedRegions(
     givenRegion=YeastRegionsChIPseq,
     bedfiles=BedFilesVector,
     motifnames=c("YeastBed1", "YeastBed2")
     )
SequenceComparison

ManchesterBioinference/Motif2Site documentation built on Feb. 13, 2022, 2:03 a.m.