reviseAnnotations-package | reviseAnnotations. |
basesDifferent | Calculate the number of bases that are different between two GRanges objects. |
calculateBasepairDifference | Calculate the total number of nucleotides that are different between two transcripts. |
constructAlternativeEvents | Construct alternative transcription events form a list of transcripts. |
constructAlternativeEventsWrapper | Apply constructAlternativeEvents() to an gene_id and metadata objects. Extend truncated transcripts first. |
constructEventMetadata | Construct event metadata |
dataFrameToGRanges | Convert a data frame into a GRanges object |
extendSingleTranscript | Extend a single transcript in one direction using exons from the reference transcript |
extendTranscriptsPerGene | Extend truncated transcripts to the longest annotated transcript. |
extractGeneData | Extract gene-specifc data from annotations data frame and exons/cdss lists. |
fillMissingInternalExons | Fill missing internal exons into alternative transcript start events |
filterTranscriptMetadata | Prepare transcript metadata before extending truncated transcripts and constructing alternative events |
flattenAlternativeEvents | Combine all alternative events into a single list with appropriate names |
identifyTranscriptGroups | Identify two groups of overlapping transcripts that share the most exons between each other |
importTranscriptMetadataFromGTF | Extract transcript metadata from Ensembl GTF file |
indentifyAddedRemovedRegions | Identify regions that are specific to one of the two transcripts. |
listIntersect | Calculate the intersection of a GRangesList object |
listUnion | Calculate the union of a GRangesList object |
makeGeneTranscriptFromExons | Construct gene or transcript annotations from exon annotations |
markLongestGencodeTranscript | For each gene in a gene metadata data frame, mark the transcript with longes sequence. |
mergeByMaxDifference | If two transcripts in a GRanges list a are not sufficiently different from each other, then keep only one. |
replaceExtendedTranscripts | Replace extended trancripts in gene-specific data list. |
reviseAnnotations | reviseAnnotations. |
splitIntoBatches | Split vector of n elements into batches |
transcriptsToAnnotations | Convert list of exons to a transcript annotations that can be exported into a GFF file. |