---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{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)
```
