Overall maximum LOD score
Find overall maximum LOD score in genome scan results, across all positions and columns.
maxlod(scan1_output, map = NULL, chr = NULL, lodcolumn = NULL)
scan1_output |
An object of class |
map |
A list of vectors of marker positions, as produced by
|
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 |
A single number: the maximum LOD score across all columns and positions for the selected chromosomes.
# 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")
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