# Perform key tests for binding motifs in sequence data

## Documentation for package ‘motifTestR’ version 1.5.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

ar_er_peaks | A set of peaks with AR and ER detected
ar_er_seq | Sequences from peaks with AR and ER detected
clusterMotifs | Assign each motif to a cluster
countClusterMatches | Find matches from a PWM cluster within an XStringSet
countPwmMatches | Count the matches to a PWM within an XStringSet
ex_pfm | Example Position Frequency Matrices
getClusterMatches | Find matches from a PWM cluster within an XStringSet
getPwmMatches | Find all PWM matches within an XStringSet
hg19_mask | Regions from hg19 with high N content
makeRMRanges | Form a set of random, matching ranges for bootstrapping or permuting
makeRMRanges-method | Form a set of random, matching ranges for bootstrapping or permuting
plotMatchPos | Plot Motif Match Positions
simSeq | Simulate sequences using optional TFBMs
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
zr75_enh | Candidate Enhancer Regions from ZR-75-1 Cells