tests/testthat/test_prepare_chi.R

In huerqiang/GeoTcgaData: Processing Various Types of Data on GEO and TCGA

test_that("can parse example prepare_chi", {
    cnv <- matrix(c(
        -1.09150, -1.47120, -0.87050, -0.50880,
        -0.50880, 2.0, 2.0, 2.0, 2.0, 2.0, 2.601962, 2.621332, 2.621332,
        2.621332, 2.621332, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,
        2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0
    ), nrow = 5)
    cnv <- as.data.frame(cnv)
    rownames(cnv) <- c("AJAP1", "FHAD1", "CLCNKB", "CROCCP2", "AL137798.3")
    colnames(cnv) <- c(
        "TCGA-DD-A4NS-10A-01D-A30U-01", "TCGA-ED-A82E-01A-11D-A34Y-01",
        "TCGA-WQ-A9G7-01A-11D-A36W-01", "TCGA-DD-AADN-01A-11D-A40Q-01",
        "TCGA-ZS-A9CD-10A-01D-A36Z-01", "TCGA-DD-A1EB-11A-11D-A12Y-01"
    )
    cnv_chi_file <- prepare_chi(cnv)
    expect_true("normalCNV" %in% colnames(cnv_chi_file))
})