findMotifs: Find motif instances with a certain mismatch number

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

Description

Find motif instances in a given genome. It gets motif strings and related allowed mismatchnumbers and returns genomewide motif instances.

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

findMotifs(
  motif,
  mismatchNumber,
  genome,
  genomeBuild,
  DB = "UCSC",
  mainCHRs = TRUE,
  firstCHR = FALSE,
  MotifLocationName = "Motif_Locations",
  limitedRegion = NA
)

Arguments

motif	motif characters in nucleotide IUPAC format
mismatchNumber	Number of mismatch allowed to match with motif
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"
mainCHRs	If true only the major chromosome are considered, if FALSE Random, Uncharacterised, and Mithocondrial chromosomes are also considered
firstCHR	If true only Chr1 is used to find motifs. Default is FALSE
MotifLocationName	The name of the file of the motif locations
limitedRegion	If specified the motifs are detected in the provided granges

Value

No return value

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