count_by_maf.Rdgiven region coordinates, the function extracts genotypes for all loci in the region, computes minor allele frequency for each marker and returns the number of loci with maf <= threshold and the number of loci maf > threshold.
count_by_maf(regions, vcf_file, maf_threshold = 0.01)
| regions | list of regions as returned by the read_regions_bed function |
|---|---|
| vcf_file | path to vcf file containing genotypes |
| maf_threshold | maf threshold for counting loci |
a tibble with region name, total count of loci, count of loci above and below the maf threshold
Marcin Kierczak <marcin.kierczak@scilifelab.se>