GxE.test: A function to run a test of interaction between a collection...

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

A function to run a test of interaction between a collection of SNPs and exposures (experimental).

Description

This function runs a permutation based test run a test of interaction between a collection of SNPs and exposure variables.

Usage

GxE.test(
  snp.cols,
  preprocessed.list,
  null.mean.vec = c(0, 0),
  null.sd.vec = c(1, 1),
  n.permutes = 10000,
  n.different.snps.weight = 2,
  n.both.one.weight = 1,
  weight.function.int = 2
)

Arguments

snp.cols	An integer vector specifying the columns in the input data containing the SNPs to be tested.
preprocessed.list	The initial list produced by function preprocess.genetic.data.
null.mean.vec	A vector of estimated null means for each of the components of the E-GADGETS fitness score. It should be set to the values of the "null.mean" element of the file "null.mean.sd.info.rds" for the observed data, that is saved by the run.gadgets function.
null.sd.vec	A vector of estimated null means for each of the components of the E-GADGETS fitness score. It should be set to the values of the "null.se" element of the file "null.mean.sd.info.rds" for the observed data, that is saved by the run.gadgets function.
n.permutes	The number of permutations on which to base the test. Defaults to 10000.
n.different.snps.weight	The number by which the number of different SNPs between a case and complement/unaffected sibling is multiplied in computing the family weights. Defaults to 2.
n.both.one.weight	The number by which the number of SNPs equal to 1 in both the case and complement/unaffected sibling is multiplied in computing the family weights. Defaults to 1.
weight.function.int	An integer used to assign family weights. Specifically, we use weight.function.int in a function that takes the weighted sum of the number of different SNPs and SNPs both equal to one as an argument, denoted as x, and returns a family weight equal to weight.function.int^x. Defaults to 2.

Value

A list of three elements:

pval

The p-value of the test.

obs.fitness.score

The fitness score from the observed data

perm.fitness.scores

A vector of fitness scores for the permuted datasets.

Examples

data(case.gxe)
data(dad.gxe)
data(mom.gxe)
data(exposure)
data(snp.annotations.mci)
pp.list <- preprocess.genetic.data(case.gxe, father.genetic.data = dad.gxe,
                               mother.genetic.data = mom.gxe,
                               ld.block.vec = rep(6, 4),
                               categorical.exposures = exposure)
 run.gadgets(pp.list, n.chromosomes = 5, chromosome.size = 3,
             results.dir = "tmp_gxe", cluster.type = "interactive",
             registryargs = list(file.dir = "tmp_reg_gxe", seed = 1300),
             n.islands = 8, island.cluster.size = 4,
             n.migrations = 1)


combined.res <- combine.islands('tmp_gxe', snp.annotations.mci, pp.list, 1)
top.snps <- as.vector(t(combined.res[1, 1:3]))
set.seed(10)
GxE.test.res <- GxE.test(top.snps, pp.list)

unlink('tmp_gxe', recursive = TRUE)
unlink('tmp_reg_gxe', recursive = TRUE)

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