cbind.scan1perm: Combine columns from multiple scan1 permutation results
In rqtl/qtl2scan: Genome Scans for QTL Experiments

Description Usage Arguments Details Value See Also Examples

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

1 2	## S3 method for class 'scan1perm' cbind(...)

...

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.

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().

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

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

# 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[,1,drop=FALSE], addcovar=covar, Xcovar=Xcovar,
                n_perm=1000, perm_Xsp=TRUE,
                chr_lengths=chr_lengths(iron$gmap))
operm2 <- scan1perm(probs, pheno[,2,drop=FALSE], addcovar=covar, Xcovar=Xcovar,
                n_perm=1000, perm_Xsp=TRUE,
                chr_lengths=chr_lengths(iron$gmap))

## End(Not run)



operm <- cbind(operm1, operm2)