Perform key tests for binding motifs in sequence data
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Documentation for package ‘motifTestR’ version 1.5.0
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 |