# Extend and revise transcript annotatons.

## Documentation for package ‘txrevise’ version 0.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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.