scan1.threshold: Significance Threshold of Genome Scan

Description Usage Arguments Details Value Examples

Description

Significance Threshold of Genome Scan

Usage

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scan1.threshold(geno, pheno, pheno.cols = 1, covar = NULL,
  procedure = c("LM", "LMM", "LOCO"), G, n.perm = 1000, alpha = 0.05,
  subjects = seq(geno$subjects), markers = seq(NROW(geno$markers)),
  keep.lods = FALSE, ...)

Arguments

geno

genotype probabilities ("genotype.probs" or "cross" object)

pheno

data frame with phenotypes

pheno.cols

selection of phenotype's column(s)

covar

(additive) covariates

procedure

procedure to do the inference, see Details

G

genetic similarity matrix or a list of genetic similarity matrices or NULL

n.perm

number of permutations

alpha

level of significance

subjects

subseting of subjects

markers

subseting of markers

keep.lods

if TRUE maximum lod values thate have been used for threshold calculation are returned as attribute 'maxlods'

...

parameters passed to genrel.matrix

Details

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

Value

numeric

Examples

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

# warning, n.perm=10 is too low for practical purposes (but fast)
scan1.threshold(fake.f2, procedure="LM", n.perm=10)
scan1.threshold(fake.f2, procedure="LMM", n.perm=10)
scan1.threshold(fake.f2, procedure="LOCO", n.perm=10)

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