build an exon count table for a gene

build an exon count table for a gene, each row is an isoform in a cell and each column is a meta-exon

Usage

extractExonTable(
  spliceOb,
  gene,
  gene_bed = NULL,
  cells = "all",
  exons = "all",
  exon_len_thresh = 10,
  sep = "|"
)

Arguments

spliceOb

the input splice object

gene

name of the target gene

gene_bed

gene bed annotation

cells

cells to use in building exon count table

exons

exon to use in building exon count table

exon_len_thresh

the minimum length of an exon to be preserved in exon count table

sep

The seperation character between exons in the isoform string

gtf

gtf annotation

Value

an exon count table for isoforms in each cell

Details

build an exon count table for a gene, each row is an isoform in a cell and each column is a meta-exon