Man pages for ProActive
Detect Elevations and Gaps in Mapped Sequencing Read Coverage
| changewindowSize | Change the pileup window size |
| classifSumm | Summarizes pattern-matching results |
| collectBestMatchInfo | Collect information regarding the pattern-match |
| contigChunks | 'chunk' long contigs |
| elevOrGapClassif | Classifies partial elevation/gap pattern-matches |
| fullElevGap | Controller function for full elevation/gap pattern-matching |
| fullElevGapShrink | Shrink the width of full elevation and gap patterns |
| geneAnnotationPlot | Gene annotation plot |
| geneAnnotationSearch | Search for gene annotations on classified contigs/chunks |
| genomeChunks | 'chunk' genomes |
| GPsInElevGaps | Detect gene predictions in elevations and gaps |
| linkChunks | Link pattern-matches on contig/genome chunks |
| noPattern | No read coverage pattern |
| partialElevGap | Controller function for partial elevation/gap... |
| partialElevGapShrink | Shrink the width of partial elevation and gap patterns |
| patternBuilder | Builds pattern-match vectors |
| patternMatcher | Controller function for pattern-matching |
| patternTranslator | Full elevation/gap pattern translator |
| pileupFormatter | Reformat input pileup file |
| plotProActiveResults | Plot results of 'ProActive()' pattern-matching |
| ProActiveDetect | Detect elevations and gaps in mapped read coverage patterns. |
| ProActive-package | *ProActive* |
| removeNoPatterns | Removes 'NoPattern' classifications from best match list |
| sampleGenomegffTSV | sampleGenomegffTSV |
| sampleGenomePileup | sampleGenomePileup |
| sampleMetagenomegffTSV | sampleMetagenomegffTSV |
| sampleMetagenomePileup | sampleMetagenomePileup |
| sampleMetagenomeResults | sampleMetagenomeResults |
