qtl2 (version 0.36)

print.summary.scan1perm: Print summary of scan1perm permutations

Description

Print summary of scan1perm permutations

Usage

# S3 method for summary.scan1perm
print(x, digits = 3, ...)

Value

Invisibly returns the input, x.

Arguments

x

Object of class "summary.scan1perm", as produced by summary_scan1perm().

digits

Number of digits in printing significance thresholds; passed to base::print().

...

Ignored.

Details

This is to go with summary_scan1perm(), so that the summary output is printed in a nice format. Generally not called directly, but it can be in order to control the number of digits that appear.

Examples

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[,c(10,18,"X")]

# 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)

# permutations with genome scan (just 3 replicates, for illustration)
operm <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar,
                   n_perm=3)

print( summary(operm, alpha=c(0.20, 0.05)), digits=8 )