check that the chromosome lengths are acceptable given recombination rates

For 'gscramble' to work properly, all variant positions on a chromosome (found in the meta data file) must be equal to or less than the total chromosome length found in the recombination map. In other words, the variant positions must be within the the total length of each chromosome. The check_chrom_lengths() function checks that variant positions on each chromosome do not exceed the total chromosome length from the recombination map. Input files for the function include 1) the meta data file which contains 3 columns (the chromosome ID as a character, the position of the variant as a numeric, and the name of the variant as a character) and 2) the recombination map which contains 5 columns (the chromosome ID as a character, the total length of the chromosome as a numeric, the starting position of the recombination bin as a numeric, the last position of the recombination bin as a numeric, and the recombination probability for the given bin as a numeric).

check_chrom_lengths(meta, rec)

Arguments

meta

a tibble with meta data for the genotype data. It must consist of the columns (chrom, pos, variant_id).

rec

a tibble with recombination map information for your study species.It must contain 5 columns (chrom, chrom_len, start_pos, end_pos, rec_prob).

Value

This function will return a message for each chromosome stating whether the chromosome lengths are accurate

Examples

# The example uses the built in datasets M_meta and RecRates
# to use the check_chrom_lengths() function

check_chrom_lengths(M_meta,RecRates)