Calculate founder minor allele frequencies from raw SNP genotypes
Calculate minor allele frequency from raw SNP genotypes in founders, by founder strain or by marker
calc_raw_founder_maf(cross, by = c("individual", "marker"))cross |
Object of class |
by |
Indicates whether to summarize by founder strain ( |
A vector of minor allele frequencies, one for each founder strain or marker.
## Not run:
# load example data and calculate genotype probabilities
file <- paste0("https://raw.githubusercontent.com/rqtl/",
"qtl2data/master/DOex/DOex.zip")
DOex <- read_cross2(file)
DOex_maf <- calc_raw_founder_maf(DOex)
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