writeREdf: Writes a data table generated by comparePeaksAltre

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

Description

Creates a CSV file containing a data table

Usage

writeREdf(comparePeaksOut, con)

Arguments

comparePeaksOut	output generated from comparePeaksAltre()
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
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"
writeREdf(comparePeaksOut, con)


## End(Not run)

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