qtl2 (version 0.32)

max_scan1: Find position with maximum LOD score

Description

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

Usage

max_scan1(
  scan1_output,
  map = NULL,
  lodcolumn = 1,
  chr = NULL,
  na.rm = TRUE,
  ...
)
# S3 method for scan1
max(scan1_output, map = NULL, lodcolumn = 1, chr = NULL, na.rm = TRUE, ...)

Value

If map is NULL, the genome-wide maximum LOD score for the selected column is returned. If also lodcolumn is NULL, you get a vector with the maximum LOD for each column.

If map is provided, the return value is a data.frame with three columns: chr, pos, and lod score. But if lodcolumn is NULL, you get the maximum for each lod score column, in the format provided by find_peaks(), so a data.frame with five columns: lodindex, lodcolumn, chr, pos, and lod.

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(). Can also be an indexed SNP info table, as from index_snps() or scan1snps().

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.

chr

Optional vector of chromosomes to consider.

na.rm

Ignored (take to be TRUE)

...

Ignored

Examples

# 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)

# 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")