Description Usage Arguments Examples
Creates three CSV files containing the results of pathenrichments for experimental, reference, and shared
1 | writePathEnrich(pathenrichOut, con)
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pathenrichOut |
output generated from pathenrich() |
con |
connection filepath |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 | ## 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')
MFenrich <- pathenrich(analysisresults = altre_peaks,
ontoltype = 'MF',
enrichpvalfilt = 0.01)
con <- "pathEnrichMF.zip"
writePathEnrich(pathenrichOut = MFenrich, con = con)
## End(Not run)
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