ribor: An R Interface for Ribo Files

context("rnaseq functions")
library(ribor)

experiments <- c("Hela_1", "Hela_2", "WT_1")
file.path <- system.file("extdata", "sample.ribo", package = "ribor")
ribo.object <- Ribo(file.path)

rnaseq_tidy <- get_rnaseq(ribo.object,
                          experiment = experiments)

rnaseq <- get_rnaseq(ribo.object,
                     tidy = FALSE,
                     experiment = experiments)

actual <- get_rnaseq(ribo.object,
                     region = c("UTR3j", "cds"),
                     tidy = FALSE,
                     experiment = experiments)


expected <-rnaseq[, -c(3, 4, 7)]

test_that("get_rnaseq = non-tidy CDS and UTR3J",
          expect_true(all(actual$CDS == expected$CDS)))

actual <- get_rnaseq(ribo.object,
                     region = c("UTR3", "cds", "utR5"),
                     tidy = FALSE,
                     experiment = experiments)

expected <-rnaseq[, -c(4, 6)]

test_that("get_rnaseq = non-tidy CDS and UTR3J",
          expect_true(all(actual$CDS == expected$CDS)))

actual   <- get_rnaseq(ribo.object,
                         tidy = TRUE,
                         region = c("UTR5"),
                         experiment = experiments)

expected <- rnaseq_tidy[as.character(rnaseq_tidy$region) == "UTR5", ]


test_that("get_rnaseq- tidy UTR5 only",
          expect_true(all(actual$count == expected$count)))

actual   <- get_rnaseq(ribo.object,
                       tidy = TRUE,
                       region = c("CDS", "utR5j"),
                       experiment = experiments)

expected <- rnaseq_tidy[as.character(rnaseq_tidy$region) %in% c("UTR5J", "CDS"), ]

test_that("get_rnaseq- tidy UTR5 and CDS",
          expect_true(all(actual$count == expected$count)))

actual   <- c(nrow(rnaseq_tidy), ncol(rnaseq_tidy))
expected <- c(45, 4)

test_that("get_rnaseq- tidy version size",
          expect_equal(actual, expected))

hela_1_rnaseq <- get_rnaseq(ribo.object,
                            tidy = FALSE,
                            experiment = "Hela_1")

actual   <- rnaseq[as.character(rnaseq$experiment) == "Hela_1", ]
expected <- hela_1_rnaseq

test_that("get_rnaseq- subsetting experiments",
          expect_equal(actual$UTR5, expected$UTR5))

actual   <- rnaseq_tidy[as.character(rnaseq_tidy$experiment) == "Hela_1" &
                        as.character(rnaseq_tidy$region) == "UTR5", 4]
actual   <- unname(actual)
actual   <- unlist(actual)

expected <- c(2.04, 3.2, 0)
error <- 1e-2

test_that("get_rnaseq- correct values",
          expect_equal(all(abs(expected - actual) <= error), TRUE))

actual   <- rnaseq[as.character(rnaseq$experiment) == "WT_1" &
                   as.character(rnaseq$transcript) == "GAPDH", c(-1,-2)]
actual   <- unlist(actual)

expected <- c(2.04, 5.3, 2.89, 1.78, 3.0)

result <- all(abs(expected - actual) <= error)

test_that("get_rnaseq- correct values",
          expect_equal(all(abs(expected - actual) <= error), expected = TRUE))

actual <- c(nrow(rnaseq), ncol(rnaseq))
expected <- c(9, 7)

test_that("get_rnaseq- non-tidy version size",
          expect_equal(actual, expected))

rnaseq <- get_rnaseq(ribo.object,
                     tidy = FALSE,
                     experiment = experiments,
                     compact = FALSE)

rnaseq_tidy <- get_rnaseq(ribo.object,
                          experiment = experiments,
                          compact = FALSE)

actual <- get_rnaseq(ribo.object,
                     region = c("UTR3j", "cds"),
                     tidy = FALSE,
                     experiment = experiments)


expected <-rnaseq[, -c(3, 4, 7)]

test_that("get_rnaseq = compact CDS and UTR3J",
          expect_true(all(actual$CDS == expected$CDS)))

actual <- get_rnaseq(ribo.object,
                     region = c("UTR3", "cds", "utR5"),
                     tidy = FALSE,
                     experiment = experiments)

expected <-rnaseq[, -c(4, 6)]

test_that("get_rnaseq = non-tidy CDS and UTR3J",
          expect_true(all(actual$CDS == expected$CDS)))

actual   <- get_rnaseq(ribo.object,
                       tidy = TRUE,
                       region = c("UTR5"),
                       experiment = experiments)

expected <- rnaseq_tidy[as.character(rnaseq_tidy$region) == "UTR5", ]


test_that("get_rnaseq- compact tidy UTR5 only",
          expect_true(all(actual$count == expected$count)))

actual   <- get_rnaseq(ribo.object,
                       tidy = TRUE,
                       region = c("CDS", "utR5j"),
                       experiment = experiments)

expected <- rnaseq_tidy[as.character(rnaseq_tidy$region) %in% c("UTR5J", "CDS"), ]

test_that("get_rnaseq- tidy UTR5 and CDS",
          expect_true(all(actual$count == expected$count)))