list_variants {seqCAT} | R Documentation |
List known variants present in SNV profiles
list_variants(profiles, known_variants)
profiles |
The SNV profiles to analyse (list) |
known_variants |
The known variants to look for (dataframe) |
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.
A dataframe containing the known variant genotypes in each profile.
# 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)