get_Ranges: Genomic ranges and locus ranges
In hyochoi/SCISSOR: Shape changes in selecting sample outliers in RNA-seq

get_Ranges

R Documentation

Genomic ranges and locus ranges

Description

This function returns genomic ranges and locus ranges in the needed format for downstream SCISSOR analysis

Usage

get_Ranges(
  Gene = NULL,
  regions = NULL,
  GTF.file = NULL,
  hg.ref = c("hg19", "hg38"),
  outputType = "part_intron"
)

Arguments

`Gene`	character(1) identifying the gene symbol, e.g. `"TP53"`
`regions`	character(1) describing genomic regions formatted as `"chr1:1-100,200-300:+"`
`outputType`	character(1) of the type of intronic region that will be included in output, with choices "whole_intron", "part_intron", or "only_exon"; the second is the default.

Value

a list of key information for the regions provided:

Gene gene symbol
gRanges ranges

Examples

regions="chr17:7571720-7573008,7573927-7574033,7576525-7576657,7576853-7576926,7577019-7577155,7577499-7577608,7578177-7578289,7578371-7578554,7579312-7579590,7579700-7579721,7579839-7579940:-"
Ranges=get_Ranges(Gene="TP53",regions=regions,outputType="part_intron")

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