max_scan1: Find position with maximum LOD score

In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description

Return data frame with the positions having maximum LOD score for a particular LOD score column

Usage

max_scan1(scan1_output, map, lodcolumn = 1, chr = NULL, na.rm = TRUE, ...)

## S3 method for class 'scan1'
max(scan1_output, map, lodcolumn = 1, chr = NULL,
  na.rm = TRUE, ...)

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().
lodcolumn	An integer or character string indicating the LOD score column, either as a numeric index or column name.
chr	Option vector of chromosomes to consider.
na.rm	Ignored (take to be TRUE)
...	Ignored

Value

A data.frame with three columns: chr, pos, and lod score.

Examples

# 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)

# maximum of first column
max(out, map)

# maximum of spleen column
max(out, map, lodcolumn="spleen")

# maximum of first column on chr 2
max(out, map, chr="2")

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