Reference

Core Functions
countPwmMatches()	Count the matches to a PWM within an XStringSet
getPwmMatches()	Find all PWM matches within an XStringSet
testMotifEnrich()	Test motif enrichment using a background set of sequences
testMotifPos()	Test for a Uniform Distribution across a set of best matches
makeRMRanges()	Form a set of random, matching ranges for bootstrapping or permuting
plotMatchPos()	Plot Motif Match Positions
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_pwm	Example Position Weight Matrices
hg19_mask	Regions from hg19 with high N content
zr75_enh	Candidate Enhancer Regions from ZR-75-1 Cells