list_variants: List known variants

In seqCAT: High Throughput Sequencing Cell Authentication Toolkit

Description

List known variants present in SNV profiles

Usage

list_variants(profiles, known_variants)

Arguments

profiles	The SNV profiles to analyse (list)
known_variants	The known variants to look for (dataframe)

Details

This is a function for listing known variants present in SNV profiles. Input is a list of profiles and a dataframe of known variants, containing at least the genomic locations ("chr" and "pos"). Any additional columns will be retained.

Value

A dataframe containing the known variant genotypes in each profile.

Examples

# Load test data
data(test_profile_1)
data(test_profile_2)

# Create some variants to analyse
known_variants <- data.frame(chr = 1, pos = 16229, gene = "DDX11L1")

# List the known variants in each profile
profiles <- list(test_profile_1, test_profile_2)
known_variants <- list_variants(profiles, known_variants)

seqCAT documentation built on Nov. 8, 2020, 7:36 p.m.