rbind.scan1perm: Combine data from scan1perm objects

In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description

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

Usage

## S3 method for class 'scan1perm'
rbind(...)

## S3 method for class 'scan1perm'
c(...)

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.

Value

The combined row-binded input, as a scan1perm object.

See Also

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

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
## Not run: 
operm1 <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar,
                n_perm=500, perm_Xsp=TRUE,
                chr_lengths=chr_lengths(iron$gmap))
operm2 <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar,
                n_perm=500, perm_Xsp=TRUE,
                chr_lengths=chr_lengths(iron$gmap))

## End(Not run)



operm <- rbind(operm1, operm2)

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