calc_raw_founder_maf: Calculate founder minor allele frequencies from raw SNP...

Description Usage Arguments Value See Also Examples

View source: R/calc_raw_summaries.R

Description

Calculate minor allele frequency from raw SNP genotypes in founders, by founder strain or by marker

Usage

1
calc_raw_founder_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 founder strain or marker.

See Also

recode_snps(), calc_raw_maf()

Examples

1
2
3
4
5
6
7
8
## 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_founder_maf(DOex)

## End(Not run)

qtl2 documentation built on Oct. 18, 2021, 1:06 a.m.