qtl2 (version 0.36)

rbind.scan1perm: Combine data from scan1perm objects

Description

Row-bind multiple scan1perm objects with the same set of columns

Usage

# S3 method for scan1perm
rbind(...)
# S3 method for scan1perm
c(...)

Value

The combined row-binded input, as an object of class "scan1perm"; see scan1perm().

Arguments

...

A set of permutation results from scan1perm() (objects of class "scan1perm"). They must have the same set of columns. If any include autosome/X chromosome-specific permutations, they must all be such.

Details

The aim of this function is to concatenate the results from multiple runs of a permutation test with scan1perm(), to assist in the case that such permutations are done on multiple processors in parallel.

See Also

cbind.scan1perm(), scan1perm(), scan1()

Examples

# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[,c("19","X")] # subset to chr 19 and 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)
operm1 <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar, n_perm=3)
operm2 <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar, n_perm=3)

operm <- rbind(operm1, operm2)