recode_snps {qtl2}

Recode SNPs by major allele

Description

For multi-parent populations with founder genotypes, recode the raw SNP genotypes so that 1 means homozygous for the major allele in the founders.

Usage

recode_snps(cross)

Arguments

cross

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

Value

The input cross object with the raw SNP genotypes recoded so that 1 is homozygous for the major alleles in the founders.

See Also

calc_raw_founder_maf(), calc_raw_maf()

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 <- recode_snps(DOex)

## End(Not run)