Extract null-model weighted overlap distribution for a gene pair

Returns the vector of weighted co-mutation values from all null-model permutations for a specific pair of genes.

Usage

overlap_pair_extract(gene1, gene2, obj)

Arguments

gene1: Name of the first gene/alteration.
gene2: Name of the second gene/alteration.
obj: SelectX object (list returned by selectX()$obj).

Value

Numeric vector of length obj$nSim with the null-model weighted overlap values for the pair.

Examples

# \donttest{
data(luad_run_data, package = "SelectSim")
result <- selectX(M = luad_run_data$M,
                  sample.class = luad_run_data$sample.class,
                  alteration.class = luad_run_data$alteration.class,
                  n.cores = 1, min.freq = 10, n.permut = 10,
                  verbose = FALSE)
genes <- rownames(result$obj$al$am$full)[1:2]
overlap_pair_extract(genes[1], genes[2], result$obj)
#> [1] 0.7692308 1.3942308 1.6526894 0.9821429 0.6451613 1.1692308 1.0918114
# }