print.summary.scan1perm: Print summary of scan1perm permutations

In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description

Print summary of scan1perm permutations

Usage

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

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.

Value

Invisibly returns the input, x.

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)

# permutations with genome scan
operm <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar,
                   n_perm=100, perm_Xsp=TRUE,
                   chr_lengths=chr_lengths(iron$gmap))

summary(operm, alpha=c(0.20, 0.05))

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

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