maxlod: Overall maximum LOD score

In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description

Find overall maximum LOD score in genome scan results, across all positions and columns.

Usage

maxlod(scan1_output, map = NULL, chr = NULL)

Arguments

scan1_output	An object of class "scan1" as returned by scan1().
map	A list of vectors of marker positions, as produced by qtl2geno::insert_pseudomarkers().
chr	Option vector of chromosomes to consider.

Value

A single number: the maximum LOD score across all columns and positions for the selected chromosomes.

Examples

## Not run: 
# load qtl2geno package for data and genoprob calculation
library(qtl2geno)

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2geno"))

# insert pseudomarkers into map
map <- insert_pseudomarkers(iron$gmap, step=1)

# calculate genotype probabilities
probs <- calc_genoprob(iron, map, error_prob=0.002)

# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)

# perform genome scan
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)

# overall maximum
maxlod(out)

# maximum on chromosome 2
maxlod(out, map, "2")

## End(Not run)

rqtl/qtl2scan documentation built on May 28, 2019, 2:36 a.m.