qtl2: recode_snps – R documentation

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recode_snps

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.

Examples

## 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 <- recode_snps(DOex)

## End(Not run)

qtl2

Quantitative Trait Locus Mapping in Experimental Crosses

v0.24

GPL-3

Authors

Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>), R Core Team [ctb]

Initial release

2020-12-16