calc_raw_maf: Calculate minor allele frequency from raw SNP genotypes

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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"))

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.

Value

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

See Also

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

Examples

## Not run: 
# 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)

## End(Not run)

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.