PureCN (version 1.0.3)

getSexFromCoverage: Get sample sex from coverage

Description

This function determines the sex of a sample by the coverage ratio of chrX and chrY. Loss of chromosome Y (LOY) can result in a wrong female call.

Usage

getSexFromCoverage(gatk.coverage, min.ratio = 20, verbose = TRUE)

Arguments

gatk.coverage

GATK coverage file or data read with readCoverageGatk.

min.ratio

Min chrX/chrY coverage ratio to call sample as female.

verbose

Verbose output.

Value

• Returns "M" for male, "F" for female, or NA if unknown.

Examples

gatk.tumor.file <- system.file("extdata", "example_tumor.txt", 
    package="PureCN")
sex <- getSexFromCoverage(gatk.tumor.file)