Description Usage Arguments Value Examples
Categorize altered peaks as experiment-specific, reference-specific, or shared
1 2 | categAltrePeaks(analysisresults, lfctypespecific = 1.5, lfcshared = 1.2,
pvaltypespecific = 0.01, pvalshared = 0.05)
|
analysisresults |
output of countanalysis() |
lfctypespecific |
log2fold change cutoff (of chromatin accessibility) for type specific enhancers/promoters |
lfcshared |
log2fold change cutoff (of chromatin accessibility) for shared enhancers/promoters |
pvaltypespecific |
p-value cutoff (of chromatin accessibility) for type specific enhancers/promoters |
pvalshared |
p-value cutoff (of chromatin accessibility) for shared enhancers/promoters |
list 1) results of countanalysis, 2) Frequences of sample type specific, shared, and ambiguous regulatory elements
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 | ## 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)
counts_consPeaks <- getCounts(annotpeaks = consPeaksAnnotated,
sampleinfo = sampleinfo,
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
)
## End(Not run)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.