List known variants present in SNV profiles
The SNV profiles to analyse (list)
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.
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# 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)
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