cbind.scan1perm: Combine columns from multiple scan1 permutation results

In qtl2: Quantitative Trait Locus Mapping in Experimental Crosses

Combine columns from multiple scan1 permutation results

Description

Column-bind multiple scan1perm objects with the same numbers of rows.

Usage

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

Arguments

...	A set of permutation results from scan1perm() (objects of class "scan1perm". If different numbers of permutation replicates were used, those columns with fewer replicates are padded with missing values NA. However, 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(), generally with different phenotypes and/or methods, to be used in parallel with rbind.scan1perm().

Value

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

See Also

rbind.scan1perm(), scan1perm(), scan1()

Examples

# 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)
operm1 <- scan1perm(probs, pheno[,1,drop=FALSE], addcovar=covar, Xcovar=Xcovar, n_perm=3)
operm2 <- scan1perm(probs, pheno[,2,drop=FALSE], addcovar=covar, Xcovar=Xcovar, n_perm=3)

operm <- cbind(operm1, operm2)

qtl2 documentation built on May 29, 2024, 11:46 a.m.