Quality-control filter for marker data

Drops markers failing a call-rate or minor-allele-frequency threshold, and (optionally) monomorphic markers, then imputes any remaining missing values.

Usage

qc_markers(geno, maf = 0.05, max_missing = 0.1, impute = TRUE)

Arguments

geno

A numeric marker matrix (individuals x markers), coded 0/1/2.

maf

Minimum minor allele frequency to keep a marker. Default 0.05.

max_missing

Maximum fraction of missing calls to keep a marker. Default 0.1.

impute

Whether to mean-impute remaining missing values. Default TRUE.

Value

A list with geno (the filtered, optionally imputed matrix) and removed (a named integer vector counting markers dropped by each rule).

Examples

sim <- simulate_population(n = 50, m = 200, seed = 1)
qc <- qc_markers(sim$geno)
dim(qc$geno)
#> [1]  50 199
qc$removed
#>   call_rate         maf monomorphic 
#>           0           1           0