Man pages for mevers/RNAModR
Functional Analysis of RNA Modifications
| AddAlpha | Add transparency to a list of hex colors |
| BuildTx | Build a custom transcriptome. |
| CheckClass | Check if object has class classType. |
| CheckClassTxLocConsistency | Check if entries of two 'txLoc' objects are consistent. |
| CheckClassTxLocRef | Check if entries of two 'txLoc' objects are based on the same... |
| CheckPkgDependencies | Check package dependencies. |
| CollapseTxBySec | Collapse entries from a 'GetTxBySec' return object. |
| Datasets | Internal raw datasets. |
| DedupeBasedOnNearestRef | De-duplicate 'GRangesList' entries based on distance. |
| DownsampleTxLoc | Downsample a 'txLoc' object. |
| EstimateCIFromBS | Calculate 95 bootstrap. |
| FilterTxLoc | Filter sections of a 'txLoc' object. |
| GenerateNull | Generate a list of null sites. |
| GetColPal | Return specific colour palette. |
| GetDistNearestStartStop | Get distance of sites to the nearest start/stop codon. |
| GetEEJunct | Get exon-exon boundary sites from reference transcriptome |
| GetGC | Calculate GC content within window around loci from a 'txLoc'... |
| GetGeneIds | Get different gene IDs. |
| GetId | Method 'GetId' for S4 object 'txLoc'. |
| GetLoci | Method 'GetLoci' for S4 object 'txLoc'. |
| GetMotifLoc | Get loci of motif(s). |
| GetNumberOfLoci | Method 'GetNumberOfLoci' for S4 object 'txLoc'. |
| GetRef | Method 'GetRef' for S4 object 'txLoc'. |
| GetRegions | Method 'GetRegions' for S4 object 'txLoc'. |
| GetRelDistNearest | Return list of nearest distances between entries from two... |
| GetSplicingSites | Get splicing sites from reference transcriptome |
| GetTxBySec | Get transcript sections. |
| GetTxDb | Download a new or load an existing reference transcriptome. |
| GetTxRegionCoordinates | Calculate transcript region starting coordinates. |
| GetTxSeq | Get sequences for transcript segments. |
| GetVersion | Method 'GetVersion' for S4 object 'txLoc'. |
| IsEmptyChar | Check if all entries in a character vector are empty. |
| LoadRefTx | Load reference transcriptome. |
| MatchFlank | Match 'flank' function argument |
| PerformSanityCheck | Perform sanity check of collapsed transcriptome. |
| PlotAbundance.generic | Generic function for plotting abundances (histograms). |
| PlotEnrichment.Generic | Generic function to perform enrichment analysis and plot... |
| PlotGC | Plot GC content. |
| PlotOverlap | Plot overlap of sites. |
| PlotRelDistDistribution | Plot distribution of relative distances. |
| PlotRelDistEnrichment | Perform enrichment analysis of relative distances. |
| PlotRelStartStopEnrichment | Enrichment analysis of sites relative to start/stop codon. |
| PlotSectionDistribution | Plot piechart of the number of loci in every transcript... |
| PlotSectionEnrichment | Perform enrichment analysis of sites per transcript region... |
| PlotSeqLogo | Plot sequence logo. |
| PlotSpatialDistribution | Plot spatial distribution of loci from a 'txLoc' object. |
| PlotSpatialEnrichment | Perform spatial enrichment analysis and plot results. |
| PlotSpatialRatio | Plot ratio of two spatial distributions. |
| ReadBED | Read BED-formatted file. |
| SafeLoad | Safe-loading an R package. |
| SmartMap | Map genome coordinates to transcript coordinates. |
| SmartMap.ToTx | Map genome coordinates to transcript coordinates. |
| SubsampleTxLoc | Subsample a 'txLoc' object. |
| TxLoc2GRangesList | Convert a 'txLoc' object to a 'GRangesList' object. |
| txLoc-accessors | 'txLoc' accessors. |
| txLoc-class | 'txLoc' object. |
| Unfactor | Unfactor entries in a 'data.frame'. |
| WriteBED | Write 'txLoc' object to a BED file. |
| WriteCSV | Write txLoc object to CSV file. |
