writeGREATpath: Writes a data generated by pathenrich

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

Description

Creates three CSV files containing the results of the pathway enrichment analysis for experiment-specific, reference-specific, and shared REs.

Usage

writeGREATpath(pathenrichOut, con)

Arguments

pathenrichOut	output generated from pathenrich()
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)
#Need to run getcounts on all chromosomes
counts_consPeaks <- getcounts(annotpeaks = consPeaksAnnotated,
                             csvfile = csvfile,
                             reference = 'SAEC')
                             #' altre_peaks <- countanalysis(counts = counts_consPeaks,
                             pval = 0.01,
                             lfcvalue = 1)
categaltre_peaks <- categAltrePeaks(altre_peaks,
                                    lfctypespecific = 1.5,
                                    lfcshared = 1.2,
                                    pvaltypespecific = 0.01,
                                    pvalshared = 0.05)
callGREAT <- runGREAT(peaks=categaltre_peaks)
pathGREAT <- processPathways(callGREAT)
con <- "GREAToutput.zip"
writeGREATpath(pathenrichOut = pathGREAT, con = con)

## End(Not run)

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