Package index • motifTestR

Core Functions

countPwmMatches(): Count the matches to a PWM within an XStringSet

getClusterMatches() countClusterMatches(): Find matches from a PWM cluster within an XStringSet

getPwmMatches(): Find all PWM matches within an XStringSet

testClusterEnrich(): Test enrichment across a cluster of motifs using a background set of sequences

testClusterPos(): Test positional bias motifs within a cluster

testMotifEnrich(): Test motif enrichment using a background set of sequences

testMotifPos(): Test for a Uniform Distribution across a set of best matches

clusterMotifs(): Assign each motif to a cluster

makeRMRanges(): Form a set of random, matching ranges for bootstrapping or permuting

plotMatchPos(): Plot Motif Match Positions

Simulation Functions

simMultiMotifs(): Simulate sequences with multiple motifs

simSeq(): Simulate sequences using optional TFBMs

Data Objects

ar_er_peaks: A set of peaks with AR and ER detected

ar_er_seq: Sequences from peaks with AR and ER detected

ex_pfm: Example Position Frequency Matrices

hg19_mask: Regions from hg19 with high N content

zr75_enh: Candidate Enhancer Regions from ZR-75-1 Cells