recenterBindingSitesAcrossExperiments: Combine binding sites across experiments

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

Description

Take experiment folder locations and experiment names and combine them into a combined matrix of motifs and ChIP-seq counts

Experiment folders must be generated either by DetectBindingSitesBed or DetectBindingSitesMotif.

Usage

recenterBindingSitesAcrossExperiments(
  expLocations,
  experimentNames,
  expName = "combinedData",
  fdrValue = 0.05,
  fdrCrossExp = 0.001
)

Arguments

expLocations	The path to the experiment folders
experimentNames	Name of the experiment to be used in combined ChIP-seq
expName	Name of the combined matrix
fdrValue	FDR cut-off to accept binding in each ChIP-seq experiments
fdrCrossExp	If no experiment fullfill this cutoff, the motif is not considered

Value

A pariwise Pearson correlation matrix across experiments

See Also

pairwisDifferential

Examples

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

# ChIP-seq datasets fe 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"
   )

# ChIP-seq datasets dpd in bed single end format
IPDpd <- c(system.file("extdata", "FUR_dpd1.bed", package="Motif2Site"),
        system.file("extdata", "FUR_dpd2.bed", package="Motif2Site"))
FURdpdBedInputStats <- 
  DetectBindingSitesBed(BedFile=FurMotifs,
   IPfiles=IPDpd, 
   BackgroundFiles=Inputs, 
   genome="Ecoli",
   genomeBuild="20080805",
   DB="NCBI",
   expName="FUR_Dpd_BedInput",
   format="BEDSE"
   )
                       

# Combine all FUR binding sites into one table
corMAT <- recenterBindingSitesAcrossExperiments(
    expLocations=c("FUR_Fe_BedInput","FUR_Dpd_BedInput"),
    experimentNames=c("FUR_Fe","FUR_Dpd"),
    expName="combinedFUR",
    )
corMAT

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