---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# Site2Target
The goal of Site2Target is to to associate sets of sites/peaks to target genes. It provides peakwise-associations to associate target genes for a given set of peaks. It also provides genewise-associations which start from genes (ex. differential expressed genes) and associate peaks/sites to these genes.
## Installation
To install this package, start R (version "4.4") and enter:
```
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Site2Target")
```
## Example
Here is an example of a peak-wise and a gene-wise association of differential genes WT vs KO of a transcription factor and binding sites of this transcription factor:
```
library(Site2Target)
## peak-wise association example
# Read gene expression coordinates
geneFile=system.file("extdata", "gene_expression.tsv",
package="Site2Target")
geneCoords <- Table2Granges(geneFile)
# Read gene expression table
geneTable <- read.table(geneFile, header=TRUE)
# Read peak coordinates of MEIS binding sites
tfFile =system.file("extdata", "MEIS_binding.tsv",
package="Site2Target")
TFCoords <- Table2Granges(tfFile)
tfTable <- read.table(tfFile, header=TRUE)
# Predict targets of MEIS using peakwise-association
pvals <- getTargetGenesPvals( geneCoordinates=geneCoords,
sites=TFCoords, distance = 50000)
topTargetNum <- 5
topTargetIndex <- order(pvals)[1:topTargetNum]
# Make a data frame of peak targets pvalues and expression logFCs
dfTopTarget <-
data.frame(name=geneTable$name[topTargetIndex],
pvalue=pvals[topTargetIndex],
exprLogC=geneTable$logFC[topTargetIndex]
)
dfTopTarget
## gene-wise association example
# Take differential genes iformation
geneDEIndices <- which((abs(geneTable$logFC)>1)==TRUE)
indicesLen <- length(geneDEIndices)
if(indicesLen >0)
{
geneTable <- geneTable[geneDEIndices,]
geneCoords <- geneCoords[geneDEIndices]
}
geneDENames <- geneTable$name
geneDElogFC <- geneTable$logFC
geneCoordsDE <- geneCoords
# Associate peaks located up to 50k bp to differential genes
stats <-
genewiseAssociation(associationBy="distance",
geneCoordinates=geneCoordsDE,
geneNames=geneDENames,
peakCoordinates=TFCoords,
distance=50000,
outFile="Gene_TF_50K")
stats
```
# Site2Target
