writeConsensusRE: Writes annotated genomic regions

In Mathelab/ALTRE: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Creates a CSV file with genomic regions annoted as TSS-proximal and TSS-distal regions. categorized by cell type

Usage

writeConsensusRE(countsPeaks, con)

Arguments

countsPeaks	output generated from getCounts()
con	connection filepath

Examples

## Not run: 
csvfile <- file.path(dir="yourfilepath", 'sampleinfo.csv')
sampleinfo <- loadCSVFile(csvfile)
samplePeaks <- loadBedFiles(sampleinfo)
consPeaks <- getConsensusPeaks(samplepeaks=samplePeaks,minreps=2)
TSSannot <- getTSS()
consPeaksAnnotated <- combineAnnotatePeaks(conspeaks = consPeaks,
                                          TSS = TSSannot,
                                          merge = TRUE,
                                          regionspecific = TRUE,
                                          distancefromTSSdist = 1500,
                                          distancefromTSSprox = 1000 )
con <- "annotatedRegions.csv"
writeConsensusRE(consPeaksAnnotated, con)

## End(Not run)

Mathelab/ALTRE documentation built on May 7, 2019, 3:41 p.m.