qtl2 (version 0.36)

calc_raw_maf: Calculate minor allele frequency from raw SNP genotypes

Description

Calculate minor allele frequency from raw SNP genotypes, by individual or by marker

Usage

calc_raw_maf(cross, by = c("individual", "marker"))

Value

A vector of minor allele frequencies, one for each individual or marker.

Arguments

cross

Object of class "cross2". For details, see the R/qtl2 developer guide.

by

Indicates whether to summarize by founder strain ("individual") or by marker.

See Also

recode_snps(), calc_raw_founder_maf(), calc_raw_het(), calc_raw_geno_freq()

Examples

if (FALSE) {
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/DOex/DOex.zip")
DOex <- read_cross2(file)
DOex_maf <- calc_raw_maf(DOex)
}