tests/testthat/test_phats.R

In dtangle: Cell Type Deconvolution from Gene Expressions

library("dtangle")

.runThisTest <- Sys.getenv("RunAllRRTests") == "yes"

if (.runThisTest) {
    
    
    Y <- matrix(c(1, 0, 1, 0, 0, 1, 0, 1), byrow = TRUE, nrow = 4)
    pure_samples <- list(1, 3)
    ml <- find_markers(Y = Y, pure_samples = pure_samples, gamma = 1)$L
    bes <- baseline_exprs(Y = Y, pure_samples = pure_samples, ml)
    
    test_that("phats are computed as expected", {
        ph <- est_phats(Y, ml, bes, gamma = 1)
        expect_equal(ph, matrix(c(2/3, 1/3, 2/3, 1/3, 1/3, 2/3, 1/3, 2/3), byrow = TRUE, 
            nrow = 4))
        ph <- est_phats(Y, ml, bes, gamma = 2)
        alpha <- 1/(1 + 2^(-0.5))
        expect_equal(ph, matrix(c(alpha, 1 - alpha, alpha, 1 - alpha, 1 - alpha, 
            alpha, 1 - alpha, alpha), byrow = TRUE, nrow = 4))
    })
    
}