tests/testthat/test_read_exprs_matrix.R

In ribiosIO: Input/Output Utilities of the 'ribios' Suite

## test read_exprs_matrix function
library(ribiosIO)
testfile.path <- system.file("extdata", package="ribiosIO")

## import gct
input.matrix <- matrix(c(1,2,3,2,3,4,3,4,5), nrow=3, byrow=TRUE, dimnames=list(c("a", "b", "c"),c("a","b","c")))
input.gct <- read_exprs_matrix(file.path(testfile.path,"test_read_exprs_matrix.gct"))
storage.mode(input.matrix) <- "integer"
storage.mode(input.gct) <- "integer" ## make the comparison easier
input.gct.removeAttr <- input.gct
attr(input.gct.removeAttr, "desc") <- NULL
stopifnot(identical(input.gct.removeAttr, input.matrix))

## import gmt
testgmt <- file.path(testfile.path, "test.gmt")
testgmt.list <- read_gmt_list(testgmt)

## import tab-separated file (without/with colname for the first column)
test_that("import tab-separated file", {
    expect_identical(read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix.tsv")),
                    input.matrix)
    expect_identical(read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_full.tsv")),
                    input.matrix)
})

## import space-separated file (without/with colname for the first column)
expect_identical(read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix.txt")),
                input.matrix)
expect_identical(read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix.txt")),
                input.matrix)

## import txt/gct files with duplicate colnames
ctxt <- read_exprs_matrix(file.path(testfile.path, "test_colnames.txt"))
stopifnot(identical(colnames(ctxt), c("S1", "S1", "S2", "S2")))
cgct <- read_exprs_matrix(file.path(testfile.path, "test_colnames.gct"))
stopifnot(identical(colnames(cgct), c("S1", "S1", "S2", "S2")))

## how to deal with multiple row names
## moaning with anyDuplicate(rnames) is a hard-coded feature of read.table

dup.mat <- matrix(c(1.1, 2.2, 3.3, 2.2, 3.3, 4.4, 3.3, 4.4, 5.5), nrow=3, byrow=TRUE, dimnames=list(c("a", "b", "a"), c("a", "b", "c")))
assertRoundIdentical <- function(x,y,digit=1L) stopifnot(identical(round(x,digit), round(y,digit)))
assertRoundIdentical(dup.mat,
                     read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_duprownames.tsv")))

assertRoundIdentical(dup.mat,
                     read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_duprownames.txt")))

assertRoundIdentical(dup.mat,
                     read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_full_duprownames.tsv")))
assertRoundIdentical(dup.mat,
                     read_exprs_matrix(file.path(testfile.path, "test_read_exprs_matrix_full_duprownames.txt")))

nonnumGct <- read_exprs_matrix(file.path(testfile.path, "test_nonnumbers.gct"))
nonnumGctExp <- matrix(c(1,2,3,
                      2,3,4,
                      4,6,1,
                      5,3,2,
                      5,3,1,
                      1,NA,2),nrow=6, byrow=TRUE,
                    dimnames=list(sprintf("Gene%d", 1:6), sprintf("Sample%d", 1:3)))
attr(nonnumGctExp, "desc") <- sprintf("G%d", 1:6)
expect_identical(nonnumGct, nonnumGctExp)

nonnumTxt <- read_exprs_matrix(file.path(testfile.path, "test_nonnumbers.txt"))
nonnumTxtExp <- matrix(c(1,2,3,
                      2,3,4,
                      4,6,1,
                      5,3,2,
                      5,NA,1,
                      1,NA,2),nrow=6, byrow=TRUE,
                    dimnames=list(sprintf("Gene%d", 1:6), sprintf("Sample%d", 1:3)))
attr(nonnumTxtExp, "desc") <- sprintf("G%d", 1:6)
expect_identical(nonnumTxt, nonnumTxtExp)