Man pages for jrboyd/peakrefine
Peak Refinement Metric Gathering and Evalutation by Motif Enrichment
| add_MotifEnrichmentResults | combine two MotifEnrichmentResults dervied from unique region... |
| bfcif | Conditionally run and cache FUN if results aren't already... |
| calcCorrMetrics | Title |
| calcMotifEnrichment | Title |
| calcSCCMetrics | Title |
| crossCorrByExtension | Calculate cross correlation by extending reads |
| crossCorrByExtensionFull | Measure cross correlation using specified frag_len for all... |
| crossCorrByRle | Calculate cross correlation by extending reads |
| crossCorrByShift | Calculate cross strand correlation using the read shift... |
| dot-calc_cross_corr | Calculate correlation between signal on DNA strands |
| dot-calc_stranded_coverage | Calculate coverage per strand |
| dot-extend_reads | extend reads to specified length in a strand sensitve way |
| dot-fetch_bam_stranded | .fetch_bam_stranded |
| dot-remove_duplicates | remove positional read duplicates from data.table |
| dot-shift_anchor | applies an anchor which controls x coordinate system 1)... |
| dot-view_gr_by_window_sample | view GRanges with score at specified window size by sampling... |
| getReadLength | get the read length from a bam file |
| harmonize_seqlengths | Ensure that regions in GRanges are compatible wtih seqlengths... |
| initialize-PeakRefiner-method | initialize a new PeakRefiner |
| PeakRefiner | constructor for PeakRefiner |
| PeakRefiner-class | class to handle peak refinement |
| pre_motif | Calculate a large motif enrichment once for later rounds of... |
| PWMEnrich.affinitySequenceSet | a non-exported method from PWMEnrich, here for stability |
| PWMEnrich.cloverScore | a non-exported method from PWMEnrich, here for stability |
| scoreMetrics | Title |
| score_motif | Assembles several metrics for a set of peaks from: 1) the... |
| subset_MotifEnrichmentResults | subset MotifEnrichmentResults by region and update statistics |
