gensim.matrix: Genetic Similarity Matrix

Description Usage Arguments Value Examples

Description

Genetic Similarity Matrix

Usage

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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

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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.