combineTranscripts: A helper for countReads function

In leetina4/LSplicing: Generates Long-reads Splicing Graph

Description

A function that helps combine all transcript exons coordinates

Usage

combineTranscripts(gList, dup, geneId = "")

Arguments

gList	A GRanges object that store new exon coordinates.
dup	A GRanges object of narrowed down reference coordinates of human genes. Only contain a target gene's protein coding exon.
geneId	A string of characters that stores the target Ensembl gene ID.

Value

A list of two GRanges ojects.

Examples

gRangesList <- GenomicRanges::GRanges()
referencesFile<- system.file("extdata", "example_refCoord.gff3",
package = "LSplicing")
refCoord <- rtracklayer::import(referencesFile)
gene <- "ENSG00000108788.11"

## Not run: 
combineTranscripts(gList = gRangesList,
                   dup = refCoord,
                   geneId = gene)

## End(Not run)

leetina4/LSplicing documentation built on Dec. 8, 2019, 1:34 p.m.