View source: R/combine.islands.R
combine.islands | R Documentation |
This function combines GADGETS results for individual islands into a single dataset.
combine.islands( results.dir, annotation.data, preprocessed.list, n.top.chroms.per.island = 1 )
results.dir |
The directory in which individual island results from
|
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 |
preprocessed.list |
The initial list produced by function
|
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. |
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".
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)
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