permute.dataset: A function to create permuted datasets for permutation based...

In mnodzenski/epistasisGA: An R package to identify multi-snp effects in nuclear family studies using the GADGETS method

A function to create permuted datasets for permutation based hypothesis testing.

Description

This function creates permuted datasets for permutation based hypothesis testing of GADGETS fitness scores.

Usage

permute.dataset(
  preprocessed.list,
  permutation.data.file.path,
  n.permutations = 100,
  bp.param = bpparam()
)

Arguments

preprocessed.list	The output list from preprocess.genetic.data for the original genetic data.
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 BiocParallel::bplapply for more details.

Value

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'.

Examples

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)

mnodzenski/epistasisGA documentation built on Jan. 17, 2023, 7:07 p.m.