Filter markers, traits or sequences

Markers (or traits) are filtered first, then samples are checked against the markers that are left.

Usage

filter_data(
  d,
  max_marker_missing = 0.2,
  min_maf = 0,
  drop_monomorphic = TRUE,
  max_sample_missing = 0.5,
  drop_empty_sites = TRUE
)

Arguments

d

A cl_data object.

max_marker_missing

Largest share of missing values allowed per marker or trait (0 to 1).

min_maf

Smallest minor allele (or band) frequency kept (marker data only).

drop_monomorphic

Drop markers or traits that do not vary.

max_sample_missing

Largest share of missing values allowed per sample.

drop_empty_sites

For aligned sequences, drop sites that are gaps in every sequence.

Value

The filtered cl_data, with a filter element recording what was removed.