compareMotifs2UserProvidedRegions: Compare a set of motifs 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 motifs and related mismatch numbers, it detects motifs and compare them with a user provided region.

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

The genome and build information should be provided and relevant BS genomes packages such as BSgenome.Mmusculus.UCSC.mm10 or BSgenome.Hsapiens.UCSC.hg38 must be installed for the used genome and builds.

Usage

compareMotifs2UserProvidedRegions(
  motifs,
  mismatchNumbers,
  genome,
  genomeBuild,
  DB = "UCSC",
  givenRegion,
  mainCHRs = TRUE
)

Arguments

motifs	a vector of motif characters in nucleotide IUPAC format
mismatchNumbers	a vector Number of mismatches allowed to match with motifs
genome	The genome name such as "Hsapiens", "Mmusculus", "Dmelanogaster"
genomeBuild	The genome build such as "hg38", "hg19", "mm10", "dm3"
DB	The database of genome build. default: "UCSC"
givenRegion	granges of user provided binding regions
mainCHRs	If true only the major chromosome are considered, if FALSE Random, Uncharacterised, and Mithocondrial chromosomes are also considered

Value

A dataframe which includes precision recall values for each motif

See Also

compareBedFiless2UserProvidedRegions

Examples

# Artificial example in Yeast
# install BSgenome.Scerevisiae.UCSC.sacCer3 prior to run this code
 yeastExampleFile=system.file("extdata", "YeastSampleMotif.bed",
                                package="Motif2Site")
YeastRegionsChIPseq <- Bed2Granges(yeastExampleFile)
SequenceComparison <- compareMotifs2UserProvidedRegions(
   givenRegion=YeastRegionsChIPseq,
   motifs=c("TGATTSCAGGANT", "TGATTCCAGGANT", "TGATWSCAGGANT"),
   mismatchNumbers=c(1,0,2),
   genome="Scerevisiae",
   genomeBuild="sacCer3"
   )
SequenceComparison

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