DetectBindingSites: Detect binding sites from motif

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

Description

DETECT Binding sites with given motif and mismatch number as well genome/build, False Discovery Rate for a given experiment name.

This function is called by both DetectBindingSitesBed and DetectBindingSitesMotif with different input.

Usage

DetectBindingSites(
  From,
  BedFile,
  motif,
  mismatchNumber,
  chipSeq,
  genome,
  genomeBuild,
  DB = "UCSC",
  fdrValue = 0.05,
  windowSize = 100,
  GivenRegion = NA,
  currentDir
)

Arguments

From	Type of motif dataset either "Motif" or "Bed"
BedFile	Motif locations in bed format file
motif	motif characters in nucleotide IUPAC format
mismatchNumber	Number of mismatches allowed to match with motifs
chipSeq	ChIP-seq alignment both IP and background in 1nt bed format files
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"
fdrValue	FDR value cut-off
windowSize	Window size around binding site. The total region would be 2*windowSize+1
GivenRegion	granges of user provided binding regions
currentDir	Directory for I/O operations

Value

A list of FRiPs, sequence statistics, and Motif statistics

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