Nothing
library(tcgsaseq)
context("Gene Set Analysis with tcgsa_seq wrapper")
test_that("Gene sets with no genes measure trigger warnings", {
rm(list = ls())
n <- 200
r <- 12
t <- matrix(rep(1:3), 4, ncol=1, nrow=r)
sigma <- 0.4
b0 <- 1
b1 <- 0 #under the null
y.tilde <- b0 + b1*t + rnorm(r, sd = sigma)
y <- t(matrix(rnorm(n*r, sd = sqrt(sigma*abs(y.tilde))), ncol=n, nrow=r) +
matrix(rep(y.tilde, n), ncol=n, nrow=r))
x <- matrix(1, ncol=1, nrow=r)
gs <- list(nrow(y) + 1:10)
expect_warning(tcgsa_seq(y, x, phi=t, genesets=gs,
Sigma_xi=matrix(1), indiv=rep(1:4, each=3), which_test="permutation",
which_weights="none", preprocessed=TRUE))
expect_warning(tcgsa_seq(y, x, phi=t, genesets=gs,
Sigma_xi=matrix(1), indiv=rep(1:4, each=3), which_test="asymptotic",
which_weights="none", preprocessed=TRUE))
})
test_that("Returned as many p-values as there are genesets", {
rm(list = ls())
n <- 200
r <- 12
t <- matrix(rep(1:3), 4, ncol=1, nrow=r)
sigma <- 0.4
b0 <- 1
b1 <- 0 #under the null
y.tilde <- b0 + b1*t + rnorm(r, sd = sigma)
y <- t(matrix(rnorm(n*r, sd = sqrt(sigma*abs(y.tilde))), ncol=n, nrow=r) +
matrix(rep(y.tilde, n), ncol=n, nrow=r))
x <- matrix(1, ncol=1, nrow=r)
res <- tcgsa_seq(y=y, x=x, phi=t, genesets=list(1:10, 11:20),
Sigma_xi=matrix(1), indiv=rep(1:4, each=3), which_test="asymptotic",
which_weights="none", preprocessed=TRUE)
expect_length(res$pvals$rawPval, n = length(res$genesets))
expect_length(res$pvals$adjPval, n = length(res$genesets))
})
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