Print summary of scan1perm permutations
Print summary of scan1perm permutations
## S3 method for class 'summary.scan1perm' print(x, digits = 3, ...)
x |
Object of class |
digits |
Number of digits in printing significance thresholds; passed to |
... |
Ignored. |
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.
Invisibly returns the input, x.
# 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)
# 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 )Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.