gensim.matrix: Genetic Similarity Matrix

In simecek/HPQTL: HPQTL

Description

Genetic Similarity Matrix

Usage

gensim.matrix(geno, procedure = c("LMM", "LOCO", "POMOLOCO", "LM"),
  gensim.normalization = "sample-variance", verbose = FALSE)

Arguments

geno	genotype probabilities ("genotype.probs" or "cross" object)
procedure	procedure of scan1 the G is calculated for
gensim.normalization	method to be used for genetic similarity matrix normalization
subjects	subseting of subjects
markers	subseting of markers

Value

square matrix (nind rows, nind columns)

Examples

data(fake.f2, package="qtl")
fake.f2 <- calc.genoprob(fake.f2)

geno <- extract.geno(fake.f2)
G <- gensim.matrix(geno)
Glist <- gensim.matrix(geno, procedure="LOCO")

simecek/HPQTL documentation built on May 29, 2019, 10 p.m.