compute_cf: Call Frequency

In mwesthues/sspredr: Single-Step Prediction

Description

compute_cf returns results from call frequency check

Usage

compute_cf(x, output = c("marker_names", "marker_callfreq"),
  missing_value = "??", call_threshold = NULL)

Arguments

x	A matrix. Genotype names are stored in rows whereas marker names are stored in columns.
output	Character vector with output options.
missing_value	Character vector providing the encoding of missing elements.
call_threshold	Numeric or complex vector specifying the call frequency threshold.

Value

If output is "marker_names" a character vector with marker names that have passed the quality check will be returned. If output is "marker_callfreq" a numeric vector with the call frequency at each marker locus will be returned.

Examples

 # Load a matrix with SNP genotypes encoded as numeric values
 data(marker_numeric)

 # Compute the call frequency
 compute_cf(marker_numeric, output = "marker_callfreq",
            missing_value = NA_real_)

 # Retrieve the marker names of all loci with a call frequency >= 0.9.
 compute_cf(marker_numeric, output = "marker_names",
            missing_value = NA_real_, call_threshold = 0.9)

mwesthues/sspredr documentation built on May 23, 2019, 10:56 a.m.