combine.islands: A function to combine GADGETS results for individual islands...

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

A function to combine GADGETS results for individual islands into a single dataset.

Description

This function combines GADGETS results for individual islands into a single dataset.

Usage

combine.islands(
  results.dir,
  annotation.data,
  preprocessed.list,
  n.top.chroms.per.island = 1
)

Arguments

results.dir	The directory in which individual island results from run.gadgets are saved.
annotation.data	A data frame containing columns 'RSID', 'REF' and 'ALT'. Column 'RSID' gives the RSIDs for the input SNPs, with the rows ordered such that the first RSID entry corresponds to the first SNP column in the data passed to function preprocess.genetic.data, the second RSID corresponds to the second SNP column, etc.
preprocessed.list	The initial list produced by function preprocess.genetic.data.
n.top.chroms.per.island	The number of top chromosomes per island to save in the final combined list. Defaults to the single top chromosome.

Value

A data.table containing the results aggregated across islands. Note these results be written to results.dir as combined.island.unique.chromosome.results.rds'. See the package vignette for more detailed descriptions of the content of each output column. Secondarily, this will concatenate all individual island results files and store them in a single file, called "all.island.results.concatenated.rds".

Examples

data(case)
data(dad)
data(mom)
data(snp.annotations)

pp.list <- preprocess.genetic.data(as.matrix(case[, 1:10]),
                               father.genetic.data = as.matrix(dad[ , 1:10]),
                               mother.genetic.data = as.matrix(mom[ , 1:10]),
                               ld.block.vec = c(10))

run.gadgets(pp.list, n.chromosomes = 4, chromosome.size = 3,
       results.dir = 'tmp',
       cluster.type = 'interactive',
       registryargs = list(file.dir = 'tmp_reg', seed = 1500),
       generations = 2, n.islands = 2, island.cluster.size = 1,
       n.migrations = 0)

combined.res <- combine.islands('tmp', snp.annotations[ 1:10, ], pp.list)

unlink("tmp", recursive = TRUE)
unlink("tmp_reg", recursive = TRUE)

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