README.md

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

output: github_document

```{r, echo = FALSE} knitr::opts_chunk$set( collapse = TRUE, comment = "#>", fig.path = "README-" )

# Motif2Site

The goal of Motif2Site is to detect transcription factor binding sites using 
motifs IUPAC sequence or bed coordinates and ChIP-seq experiments in bed or bam
format. It also Combines/compares binding sites across experiments, tissues, or 
conditions.

## Installation

To install this package, start R (version "4.1") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Motif2Site")

## Example

This is a basic example which shows Motif2Site detects binding sites across 
tissue and combines/compares them:

library(Motif2Site) library(BSgenome.Ecoli.NCBI.20080805)

FUR candidate motifs in NC_000913 E. coli

FurMotifs = system.file("extdata", "FurMotifs.bed", package="Motif2Site")

ChIP-seq FUR fe datasets binding sites from user provided bed file

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" )

ChIP-seq FUR dpd datasets binding sites from user provided bed file

ChIP-seq datasets 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 FUR binding sites from bed input into one table

corMAT <- recenterBindingSitesAcrossExperiments( expLocations=c("FUR_Fe_BedInput","FUR_Dpd_BedInput"), experimentNames=c("FUR_Fe","FUR_Dpd"), expName="combinedFUR" ) corMAT

FurTable <- read.table(file.path("combinedFUR","CombinedMatrix"), header = TRUE, check.names = FALSE ) FurBindingTotal <- GRanges(seqnames=Rle(FurTable[,1]), ranges = IRanges(FurTable[,2], FurTable[,3]) ) FurFe <- FurBindingTotal[which((FurTable$FUR_Fe_binding =="Binding")==TRUE)] FurDpd <- FurBindingTotal[which((FurTable$FUR_Dpd_binding =="Binding")==TRUE)] findOverlaps(FurFe,FurDpd)

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)

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