readIntervalFile: Read interval file

In lima1/PureCN: Copy number calling and SNV classification using targeted short read sequencing

Read interval file

Description

Read file containing coordinates of on- and off-target intervals generated by preprocessIntervals.

Usage

readIntervalFile(interval.file, strict = TRUE, verbose = TRUE)

Arguments

interval.file	A mapping file that assigns GC content and gene symbols to each exon in the coverage files. Used for generating gene-level calls. First column in format CHR:START-END. Second column GC content (0 to 1). Third column gene symbol. This file is generated with the preprocessIntervals function.
strict	Error out with missing columns
verbose	Verbose output

Value

A GRanges object with the parsed intervals.

Author(s)

Markus Riester

Examples

interval.file <- system.file("extdata", "example_intervals.txt", 
    package = "PureCN")
x <- readIntervalFile(interval.file)

lima1/PureCN documentation built on Sept. 17, 2024, 5:48 a.m.