DetectBindingSitesBed: Detect binding sites from bed motif input

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

Description

Takes user provied bed regions, and check for validity of them. Read bam or bed alignment files and convert to 1 nt bed and call detect binding site from 1nt bed.

Usage

DetectBindingSitesBed(
  BedFile,
  IPfiles,
  BackgroundFiles,
  genome,
  genomeBuild,
  DB = "UCSC",
  fdrValue = 0.05,
  expName = "Motif_Centric_Peaks",
  windowSize = 100,
  format = ""
)

Arguments

BedFile	Motif locations in bed format file
IPfiles	IP ChIP-seq alignment files
BackgroundFiles	Background ChIP-seq alignment files. Can be Input experimetn, DNA whole exctract, etc.
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
expName	The name of the output table
windowSize	Window size around binding site. The total region would be 2*windowSize+1
format	alignment format and should be one of these: "BAMPE", "BAMSE", "BEDPE", "BEDSE"

Value

peakCallingStatistics A list FRiPs, sequence statistics, and Motif statistics

See Also

DetectBindingSitesMotif

Examples

# FUR candidate motifs in NC_000913 E. coli
FurMotifs=system.file("extdata", "FurMotifs.bed", package="Motif2Site")

# ChIP-seq datasets in bed single end format
IPFe <- c(system.file("extdata", "FUR_fe1.bed", package="Motif2Site"),
        system.file("extdata", "FUR_fe2.bed", package="Motif2Site"))
Inputs <- c(system.file("extdata", "Input1.bed", package="Motif2Site"),
            system.file("extdata", "Input2.bed", package="Motif2Site"))
FURfeBedInputStats <- 
  DetectBindingSitesBed(BedFile=FurMotifs,
                        IPfiles=IPFe, 
                        BackgroundFiles=Inputs, 
                        genome="Ecoli",
                        genomeBuild="20080805",
                        DB="NCBI",
                        expName="FUR_Fe_BedInput",
                        format="BEDSE"
                       )

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