build_pileup: Build coverage pileup based on annotations
In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

build_pileup

R Documentation

Build coverage pileup based on annotations

Description

This function is used to get pileup data based on new transcript for the purpose of the downstream outlier detection analysis.

Usage

build_pileup(
  Pileup,
  caseIDs = NULL,
  regions,
  inputType = "part_intron",
  outputType = "part_intron"
)

Arguments

`regions`	genomic regions formatted as chr1:1-100,200-300:+"
`inputType`	type of intronic region contained in pileup, with choices "whole_intron", "part_intron", or "only_exon"; the first is the default.
`outputType`	type of intronic region that will be included in output, with choices "whole_intron", "part_intron", or "only_exon"; the second is the default.

Examples

regions = "chrQ:7571719-7572198,7574858-7575157,7598088-7598437:-"
countPileup = build_pileup(Pileup=paste0(package_path,"SCISSOR/toydata/TOY_coverage.txt"),inputType="whole_intron",caseIDs=NULL,regions=regions)

hyochoi/SCISSOR documentation built on July 6, 2022, 6:59 a.m.