Tools for spliced gene structure manipulation and analysis


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Documentation for package ‘GeneStructureTools’ version 1.2.1

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addBroadTypes Change transcript biotypes to a broader set
addIntronInTranscript Add a retained intron to the transcripts it is skipped by
alternativeIntronUsage Create transcripts with alternative intron usage
annotateGeneModel Annotate a GRanges gene model with ORF boundries for visualisation with Gviz
attrChangeAltSpliced Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts
coordinates Method coordinates
coordinates-method Method coordinates
DEXSeqIdsToGeneIds Convert DEXSeq ids to gene ids
diffSplicingResults Method diffSplicingResults
diffSplicingResults-method Method diffSplicingResults
exonsToTranscripts Convert an exon-level gtf annotation to a transcript-level gtf annotation
filterGtfOverlap Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR
filterWhippetEvents Filter out significant events from a whippet diff comparison
findDEXexonType Find a DEXSeq exons' biotype
findExonContainingTranscripts Given the location of a whole spliced in exon, find transcripts which can splice out this exon
findIntronContainingTranscripts Given the location of a whole retained intron, find transcripts which splice out this intron
findJunctionPairs Find alternative junctions for Whippet alternative splicing events
formatWhippetEvents Format Whippet co-ordinates as a GRanges object
getOrfs Get open reading frames for transcripts
getUOrfs Get upstream open reading frames for transcripts with annotated main ORFs
junctions Method junctions
junctions-method Method junctions
leafcutterTranscriptChangeSummary Compare open reading frames for whippet differentially spliced events
makeGeneModel Convert GRanges gene model to data.frame for visualisation with Gviz
maxLocation Find the largest distance between two vectors of numbers Helper function for get_orfs
orfDiff Evaluate changes to ORFs caused by alternative splicing
orfSimilarity calculate percentage of orfB contained in orfA
overlapTypes Annotate introns and exonic parts by overlaping exon biotype
readCounts Method readCounts
readCounts-method Method readCounts
readWhippetDataSet Import whippet results files as a whippetDataSet
readWhippetDIFFfiles Read in a list of whippet .diff.gz files and format as a data.frame
readWhippetJNCfiles Read in a list of whippet .jnc.gz files and format as a GRanges object
readWhippetPSIfiles Read in a list of whippet .psi.gz files and format as a data.frame
removeDuplicateTranscripts Remove transcript duplicates
removeSameExon Remove exon duplicates
removeVersion Remove version number from ensembl gene/transcript ids
reorderExonNumbers Reorder the exon numbers in a gtf annotation
replaceJunction Find transcripts containing/overlapping junctions and replace them with alternative junctions
skipExonInTranscript Remove and include a skipped exon from the transcripts it overlaps
summariseExonTypes Summarise exon biotypes to broader categories
transcriptChangeSummary Compare open reading frames for two sets of paired transcripts
UTR2UTR53 Annotate UTRs from Gencode GTF as 5' or 3'
whippetDataSet-class Class whippetDataSet
whippetTranscriptChangeSummary Compare open reading frames for whippet differentially spliced events