pairwisDifferential: Detect differential motifs

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

Description

Take combined matrix of motif counts generated by recenterBindingSitesAcrossExperiments, and experiment names. It detect differential motifs using edgeR TMM nomralizaiton with Generalized linear model

Usage

pairwisDifferential(
  tableOfCountsDir = "",
  exp1,
  exp2,
  FDRcutoff = 0.05,
  logFCcuttoff = 1
)

Arguments

tableOfCountsDir	Directory which conatins the combined motifs and ChIP-seq count file
exp1	Experiment name which will be compared in pairwise comparison
exp2	Experiment name which will be compared in pairwise comparison
FDRcutoff	FDR cutoff applies on pvalue distribution
logFCcuttoff	log fold change cutoff

Value

A list of differential motifs, motif1 and motif2 as well as a table of total motifs and log fold changes

See Also

recenterBindingSitesAcrossExperiments

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",
  )

# Differential binding sites across FUR conditions fe vs dpd
diffFUR <- pairwisDifferential(tableOfCountsDir="combinedFUR",
   exp1="FUR_Fe",
   exp2="FUR_Dpd",
   FDRcutoff=0.05,
   logFCcuttoff=1
   )

FeUp <- diffFUR[[1]]
DpdUp <- diffFUR[[2]]
TotalComparison <- diffFUR[[3]]
head(TotalComparison)

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