writeAnnotatedRegions: Writes annotated genomic regions

In ewymathe/testALTREinstall: Workflow for Identifying Regulatory Elements from Chromatin Accessibility Assay Data

Description

Creates a CSV file with genomic regions annoted as promotor or enhances categorized by cell type

Usage

writeAnnotatedRegions(countsPeaks, con)

Arguments

countsPeaks	output generated from getCounts()
con	connection filepath

Examples

## Not run: 
dir <- system.file('extdata', package='ALTRE', mustWork=TRUE)
csvfile <- file.path(dir, 'lung.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,
                                          mergedistenh = 1500,
                                          mergedistprom = 1000 )
#Need to run getcounts on all chromosomes
countsPeaks <- getcounts(annotpeaks = consPeaksAnnotated,
                             csvfile = csvfile,
                             reference = 'SAEC')
con <- "annotatedRegions.csv"
writeAnnotatedRegions(countsPeaks, con)

## End(Not run)

ewymathe/testALTREinstall documentation built on May 16, 2019, 9:42 a.m.