list_variants {seqCAT} | R Documentation

## List known variants

### 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)

[Package seqCAT version 1.14.1 Index]