maxlod: Overall maximum LOD score

Description Usage Arguments Value Examples

View source: R/max_scan1.R

Description

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

Usage

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

Arguments

scan1_output

An object of class "scan1" as returned by scan1().

map

A list of vectors of marker positions, as produced by insert_pseudomarkers().

chr

Optional vector of chromosomes to consider.

lodcolumn

An integer or character string indicating the LOD score column, either as a numeric index or column name. If NULL, return maximum for all columns.

Value

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

Examples

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# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))

# 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")

qtl2 documentation built on Oct. 18, 2021, 1:06 a.m.