writeCompareRE: Writes a data table generated by comparePeaksAltre

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

Description

Creates a CSV file with the number of peaks called as experiment- or reference-specific and shared using the quantitative/peak intensity or peak/binary approach.

Usage

writeCompareRE(comparePeaksOut, con)

Arguments

comparePeaksOut	output generated from comparePeaksAltre()
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)
comparePeaksOut <- comparePeaksAltre(categaltre_peaks, reference= 'SAEC')
con <- "datatableRE.csv"
writeCompareRE(comparePeaksOut, con)


## End(Not run)

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