Combine data from scan1perm objects
Row-bind multiple scan1perm objects with the same set of columns
## S3 method for class 'scan1perm' rbind(...) ## S3 method for class 'scan1perm' c(...)
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A set of permutation results from
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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.
The combined row-binded input, as an object of class "scan1perm"; see scan1perm().
# 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, addcovar=covar, Xcovar=Xcovar, n_perm=3)
operm2 <- scan1perm(probs, pheno, addcovar=covar, Xcovar=Xcovar, n_perm=3)
operm <- rbind(operm1, operm2)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.