Extend and revise transcript annotatons.


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Documentation for package ‘txrevise’ version 0.1

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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.