scan1: Genome Scan With a Single QTL Model

In simecek/HPQTL: HPQTL

Description

Genome Scan With a Single QTL Model

Usage

scan1(geno, pheno, pheno.col = 1, rankZ = FALSE, covar = NULL,
  intcovar = NULL, procedure = c("LM", "LMM", "LOCO"), G, verbose = FALSE,
  Intercept = rep(1, length(geno$subjects)), ...)

Arguments

geno	genotype probabilities ("genotype.probs" or "cross" object)
pheno	data frame with phenotypes
covar	(additive) covariates
intcovar	interactive covariates (interact with QTL genotype)
procedure	procedure to do the inference, see Details
G	genetic similarity matrix or a list of genetic similarity matrices or NULL
Intercept	option to pass rotated intercept for LMM model
...	parameters passed to gensim.matrix
pheno.cols	selection of phenotype's column(s)

Details

Currently, three procedures are implemented: linear model (LM), linear mixed model (LMM) and linear mixed model - leave one chromosome out (LOCO).

Value

scanone object

Examples

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

plot(scan1(fake.f2, procedure="LM"), incl.markers=FALSE)
plot(scan1(fake.f2, procedure="LMM"), incl.markers=FALSE)
plot(scan1(fake.f2, procedure="LOCO"), incl.markers=FALSE)

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