max_scan1: Find position with maximum LOD score

In rqtl/qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

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 class 'scan1'
max(scan1_output, map = NULL, 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 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

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.

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")

rqtl/qtl2 documentation built on March 20, 2024, 6:35 p.m.