View source: R/permute.dataset.R
permute.dataset | R Documentation |
This function creates permuted datasets for permutation based hypothesis testing of GADGETS fitness scores.
permute.dataset( preprocessed.list, permutation.data.file.path, n.permutations = 100, bp.param = bpparam() )
preprocessed.list |
The output list from |
permutation.data.file.path |
If running GADGETS for GxG interactions, this argument specifies a directory where each permuted dataset will be saved on disk. If searching for GxE interactions, permuted versions of the exposure matrix will be saved to this directory. |
n.permutations |
The number of permuted datasets to create. |
bp.param |
The BPPARAM argument to be passed to bplapply.
See |
If genetic data are specified, a total of n.permutations
datasets containing pairs of case and complement data, where the observed
case/complement status has been randomly flipped or not flipped, will be
saved to permutation.data.file.path
. If exposure data are specified, a
total of n.permutations
exposure matrices, where the observed
exposures have been randomly re-assigned across the permuted 'families'.
data(case) case <- as.matrix(case) data(dad) dad <- as.matrix(dad) data(mom) mom <- as.matrix(mom) pp.list <- preprocess.genetic.data(case[, 1:10], father.genetic.data = dad[ , 1:10], mother.genetic.data = mom[ , 1:10], ld.block.vec = c(10)) set.seed(15) perm.data.list <- permute.dataset(pp.list, "tmp_perm", n.permutations = 1) unlink("tmp_perm", recursive = TRUE)
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