Man pages for jsemple19/nanodsmf
Analyse nanopore dual enzyme single molecule footprinting data (nanoDSMF)
| applyGRonGR | Apply a function on a data from gr2 with windows provided by... |
| BSgenomeToDNAStringSet | Convert BSgenome to DNAStringSet |
| BSgenomeToGR | Convert BSgenome to GenomicRanges |
| DNAStringSetToGR | Convert DNAStringSet to GenomicRanges |
| findGenomeMotifs | Find non overlapping CG, GC and GCG/CGC motifs in genome |
| findNonOverlappingMotifs | Finds all CG, GC and long GCGC stretches in DNAStringSet |
| getIsolatedSites | Adds unique sites from first GRanges that are not in the... |
| getOverlappingSites | Adds overlapping sites from first GRanges to the second |
| MCviPI_CpG | Example of calling CpG methylation on GpC methylated amplicon |
| MCviPI_freqCmG | Example of calling CpG methylation on GpC methylated amplicon |
| MCviPI_freqGCm | Example of calling GpC methylation on GpC methylated amplicon |
| MCviPI_GpC | Example of calling GpC methylation on GpC methylated amplicon |
| mergeCGandGCmat | Merge CG and GC methylation matrices |
| mergeCGandGCtsv | Merge CG tsv and GC tsv |
| mIdxToGR | Convert MIndex object to Genomic Ranges object |
| MSssI_CpG | Example of calling CpG methylation on CpG methylated amplicon |
| MSssI_freqCmG | Example of calling CpG methylation on CpG methylated amplicon |
| MSssI_freqGCm | Example of calling GpC methylation on CpG methylated amplicon |
| MSssI_GpC | Example of calling GpC methylation on CpG methylated amplicon |
| plotSingleMoleculesAmp | Do a single molecule plot of dSMF data |
| splitGCGCruns | Splits GenomicRange into multiple ranges of width 2 or 3. |
| splitMotifs | Split sequences with multiple motifs |
| splitRangeInPairs | Splits GenomicRange into multiple ranges of width 2. |
| tsvToGR | Convert nanopore tsv to genomic ranges |
| tsvToMethMat | Convert nanopore tsv to methylation matrix |
| ttTi5605dna | DNAstringset for sequence used in example data |
| ttTi5605gr | GenomicRanges for sequence used in example data |
| ucscToWbGR | Convert UCSC to wormbase chromosome names |
| wbToUcscGR | Convert wormbase to ucsc chromosome names |
