closestExonToJunctions: Find closest exon to splice junction ends

In jmw86069/splicejam: Analysis and Visualization of Gene Splice Variants and Transcriptome Data

Find closest exon to splice junction ends

Description

Find closest exon to splice junction ends

Usage

closestExonToJunctions(
  spliceGRgene,
  exonsGR,
  flipNegativeStrand = TRUE,
  sampleColname = "sample_id",
  reportActualCoords = FALSE,
  spliceBuffer = NULL,
  verbose = FALSE,
  ...
)

Arguments

spliceGRgene	GRanges representing splice junctions
exonsGR	GRanges representing flattened exons per gene, as is produced by flattenExonsBy().
flipNegativeStrand	logical indicating whether to flip the orientation of features on the negative strand.
sampleColname	character value matching the colname that defines distinct sample identifier, for which junctions will be kept separate.
reportActualCoords	logical indicating whether to report genomic coordinates or transcriptome coordinates. (Work in progress.)
spliceBuffer	optional integer indicating the maximum distance from an exon in order for an exon to be assigned to the exon. When spliceBuffer=NULL the distance is ignored in value columns c("nameFrom","nameTo"). When spliceBuffer is supplied, and junction is greater than this distance, the value columns c("nameFrom","nameTo") will indicate the exon name appended to the distance.
verbose	logical indicating whether to print verbose output.
...	additional arguments are ignored.

Details

This function is used to annotate splice junction GRanges entries based upon the closest compatible stranded exon boundary.

This function should usually be called by spliceGR2junctionDF() and not called directly.

See Also

Other jam RNA-seq functions: assignGRLexonNames(), combineGRcoverage(), defineDetectedTx(), detectedTxInfo(), exoncov2polygon(), flattenExonsBy(), getGRcoverageFromBw(), groups2contrasts(), internal_junc_score(), makeTx2geneFromGtf(), make_ref2compressed(), prepareSashimi(), runDiffSplice(), sortSamples(), spliceGR2junctionDF()

Other jam GRanges functions: addGRLgaps(), addGRgaps(), annotateGRLfromGRL(), annotateGRfromGR(), assignGRLexonNames(), combineGRcoverage(), exoncov2polygon(), findOverlapsGRL(), flattenExonsBy(), getFirstStrandedFromGRL(), getGRLgaps(), getGRcoverageFromBw(), getGRgaps(), grl2df(), jam_isDisjoint(), make_ref2compressed(), sortGRL(), spliceGR2junctionDF(), stackJunctions()

jmw86069/splicejam documentation built on Nov. 4, 2024, 10:53 a.m.