View source: R/compute.graphical.scores.R
compute.graphical.scores | R Documentation |
This function returns a data.table of graphical SNP-pair scores for use in network plots of GADGETS results.
compute.graphical.scores(
results.list,
preprocessed.list,
score.type = "logsum",
pval.thresh = 0.05,
n.permutes = 10000,
n.different.snps.weight = 2,
n.both.one.weight = 1,
weight.function.int = 2,
recessive.ref.prop = 0.75,
recode.test.stat = 1.64,
bp.param = bpparam(),
null.mean.vec.list = NULL,
null.sd.vec.list = NULL
)
results.list |
A list of length d, where d is the number of
chromosome sizes to be included in the network plot. Each element of the list
should be a data.table from |
preprocessed.list |
The list output by |
score.type |
A character string specifying the method for aggregating
SNP-pair scores across chromosome sizes. Options are 'max', 'sum', or
'logsum', defaulting to 'logsum'. For a given SNP-pair, it's graphical score
will be the |
pval.thresh |
A numeric value between 0 and 1 specifying the epistasis
test p-value threshold for a chromosome to contribute to the network. Any
chromosomes with epistasis p-value greater than |
n.permutes |
The number of permutations on which to base the epistasis tests. 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 |
recessive.ref.prop |
The proportion to which the observed proportion of informative cases with the provisional risk genotype(s) will be compared to determine whether to recode the SNP as recessive. Defaults to 0.75. |
recode.test.stat |
For a given SNP, the minimum test statistic required to recode and recompute the fitness score using recessive coding. Defaults to 1.64. |
bp.param |
The BPPARAM argument to be passed to bplapply.
See |
null.mean.vec.list |
(experimental) A list, equal in length to
|
null.sd.vec.list |
(experimental) A list, equal in length to
|
A list of two elements:
A data.table containing SNP-pair graphical scores, where the first four columns represent SNPs and the fifth column (pair.score) is the graphical SNP-pair score.
A data.table containing individual SNP graphical scores, where the first two columns represent SNPs and the third column (snp.score) is the graphical SNP score.
data(case)
data(dad)
data(mom)
data(snp.annotations)
set.seed(1400)
# preprocess data
target.snps <- c(1:3, 30:32, 60:62, 85)
preprocessed.list <- preprocess.genetic.data(as.matrix(case[, target.snps]),
father.genetic.data = as.matrix(dad[ , target.snps]),
mother.genetic.data = as.matrix(mom[ , target.snps]),
ld.block.vec = c(3, 3, 3, 1))
## run GA for observed data
#observed data chromosome size 2
run.gadgets(preprocessed.list, n.chromosomes = 5, chromosome.size = 2,
results.dir = 'tmp_2',
cluster.type = 'interactive',
registryargs = list(file.dir = 'tmp_reg', seed = 1500),
generations = 2, n.islands = 2, island.cluster.size = 1,
n.migrations = 0)
combined.res2 <- combine.islands('tmp_2',
snp.annotations[ target.snps, ], preprocessed.list, 2)
unlink('tmp_reg', recursive = TRUE)
#observed data chromosome size 3
run.gadgets(preprocessed.list, n.chromosomes = 5,
chromosome.size = 3, results.dir = 'tmp_3',
cluster.type = 'interactive',
registryargs = list(file.dir = 'tmp_reg', seed = 1500),
generations = 2, n.islands = 2, island.cluster.size = 1,
n.migrations = 0)
combined.res3 <- combine.islands('tmp_3', snp.annotations[ target.snps, ],
preprocessed.list, 2)
unlink('tmp_reg', recursive = TRUE)
## create list of results
final.results <- list(combined.res2[1:3, ], combined.res3[1:3, ])
## compute edge scores
edge.dt <- compute.graphical.scores(final.results,
preprocessed.list,
pval.thresh = 0.5)
lapply(c("tmp_2", "tmp_3"), unlink, recursive = TRUE)
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