DetectBindingSitesMotif: Detect binding sites from sequence motif sequence and...

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. Read bam or bed alignment files and convert to 1 nt bed and detect binding site among motifs from 1nt bed alignment.

Usage

DetectBindingSitesMotif(
  motif,
  mismatchNumber,
  IPfiles,
  BackgroundFiles,
  genome,
  genomeBuild,
  DB = "UCSC",
  fdrValue = 0.05,
  expName = "Motif_Centric_Peaks",
  windowSize = 100,
  format = "",
  GivenRegion = NA
)

Arguments

motif	motif characters in nucleotide IUPAC format
mismatchNumber	Number of mismatches allowed to match with motifs
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"
GivenRegion	granges of user provided binding regions

Value

A list FRiPs, sequence statistics, and Motif statistics

See Also

DetectBindingSitesBed

Examples

# 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"))

 # Granages region for motif search           
   NC_000913_Coordiante <-
     GenomicRanges::GRanges(seqnames=S4Vectors::Rle("NC_000913"),
                            ranges=IRanges::IRanges(1, 4639675))           
            
FURfeStringInputStats <- 
  DetectBindingSitesMotif(motif="GWWTGAGAA",
   mismatchNumber=1,
   IPfiles=IPFe, 
   BackgroundFiles=Inputs, 
   genome="Ecoli",
   genomeBuild="20080805",
   DB="NCBI",
   expName="FUR_Fe_StringInput",
   format="BEDSE",
   GivenRegion=NC_000913_Coordiante 
   )

                                      

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