customEnrichment.RdThis function will perform hypergeometric enrichment of a given peak matches object and ranges.
customEnrichment(ranges = NULL, matches = NULL, bgdPeaks = NULL)A GenomicRanges object of peaks/regions to overlap with peaks.
A custom peakAnnotation matches object used as input for the hypergeometric test. See
motifmatchr::matchmotifs() for additional information.
A SummarizedExperiment of background peaks from getBgdPeaks can be NULL for using all peaks.
#Project
proj <- getTestProject()
#Get Peaks
peaks <- getPeakSet(proj)
#Custom C1 Mono
peaks1 <- peaks[names(peaks)=="C1"]
#All Peaks
customEnrichment(
ranges = peaks1,
matches = getMatches(proj)
)
# feature CompareFrequency nCompare CompareProportion BackgroundFrequency
# CEBPB_1 CEBPB_1 70 635 0.11023622 122
# CEBPA_2 CEBPA_2 81 635 0.12755906 156
# IRF4_4 IRF4_4 103 635 0.16220472 276
# EOMES_6 EOMES_6 36 635 0.05669291 120
# ETS1_3 ETS1_3 38 635 0.05984252 149
# PAX5_5 PAX5_5 23 635 0.03622047 124
# nBackground BackgroundProporition Enrichment mlog10p mlog10Padj
# CEBPB_1 2142 0.05695612 1.9354589 10.3279 9.373657
# CEBPA_2 2142 0.07282913 1.7514839 8.9394 7.985157
# IRF4_4 2142 0.12885154 1.2588497 2.6938 1.739557
# EOMES_6 2142 0.05602241 1.0119685 0.3001 0.000000
# ETS1_3 2142 0.06956116 0.8602864 0.0487 0.000000
# PAX5_5 2142 0.05788982 0.6256795 0.0006 0.000000
#Background Peaks
customEnrichment(
ranges = peaks1,
matches = getMatches(proj),
bgdPeaks = getBgdPeaks(proj, force=TRUE)
)
# feature CompareFrequency nCompare CompareProportion BackgroundFrequency
# CEBPB_1 CEBPB_1 70 635 0.11023622 2459
# CEBPA_2 CEBPA_2 81 635 0.12755906 3154
# IRF4_4 IRF4_4 103 635 0.16220472 4836
# ETS1_3 ETS1_3 38 635 0.05984252 1781
# EOMES_6 EOMES_6 36 635 0.05669291 1975
# PAX5_5 PAX5_5 23 635 0.03622047 1495
# nBackground BackgroundProporition Enrichment mlog10p mlog10Padj
# CEBPB_1 32385 0.07593021 1.4518097 2.9544 2.000157
# CEBPA_2 32385 0.09739077 1.3097654 2.1341 1.179857
# IRF4_4 32385 0.14932839 1.0862283 0.7142 0.000000
# ETS1_3 32385 0.05499460 1.0881527 0.4975 0.000000
# EOMES_6 32385 0.06098502 0.9296203 0.1551 0.000000
# PAX5_5 32385 0.04616335 0.7846154 0.0422 0.000000
#