Explore locus coverage prior to filtering — explore_filter_coverage

Explore what effect the filter_coverage_loci() function will have on the data without actually applying any filters. Can be used to set coverage thresholds.

explore_filter_coverage_loci(
  x,
  min_coverage = 5,
  max_low_coverage = 50,
  breaks = 100
)

Arguments

x: object of class mipanalyzer_biallelic or mipanalyzer_multiallelic.
min_coverage: the coverage threshold below which data is deemed to be low-coverage.
max_low_coverage: (percentage). Loci are not allowed to contain more than this many low-coverage samples. In the filter_coverage_loci() function, any locus with more than max_low_coverage low-coverage samples will be dropped.
breaks: number of breaks spanning the range [0,100].