tests/testthat/test_munge.R

In jvwong/emRNASeq: Utilities for RNA sequencing analysis

library(emRNASeq)

context("metadata munging")

### merge_data
data_dir <- file.path(getwd(), "data")
gene_model <- readRDS(file.path(data_dir, "mock_gene_model.rds"))
metadata_file <- file.path(data_dir, "tep_phenotypes.txt")
filelist <- c(file.path(data_dir, "MGH-BrCa-H-74_htsqct.txt"),
  file.path(data_dir, "MGH-BrCa-H-68_htsqct.txt"),
  file.path(data_dir, "MGH-BrCa-H-66_htsqct.txt"),
  file.path(data_dir, "MGH-BrCa-H-59_htsqct.txt"),
  file.path(data_dir, "MGH-BrCa-H-11_htsqct.txt"),
  file.path(data_dir, "HD-5_htsqct.txt"),
  file.path(data_dir, "HD-4_htsqct.txt"),
  file.path(data_dir, "HD-3-1_htsqct.txt"),
  file.path(data_dir, "HD-2-1_htsqct.txt"),
  file.path(data_dir, "HD-1_htsqct.txt"))

source_name <- "ensembl_gene_id"
target_name <- "hgnc_symbol"
species <- "human"

test_that("merge_data requires correct parameters", {
  expect_error(merge_data(metadata_file, species = 3.2,  source_name, target_name, filelist))
})

with_mock(
  get_gene_model = function( data_df, species, source_name, target_name ){ gene_model },
  sample_merged_se <- emRNASeq::merge_data(metadata_file, species, source_name, target_name, filelist)
)

test_that("merge_data produes a SummarizedExperiment", {
  expect_is(sample_merged_se, "SummarizedExperiment")
})

test_that("merge_data result has data", {
  expect_gt(dim(SummarizedExperiment::assays(sample_merged_se)$counts)[1], 30000)
  expect_equal(dim(SummarizedExperiment::colData(sample_merged_se)), c(length(filelist),1))
  expect_gt(dim(SummarizedExperiment::rowData(sample_merged_se))[1], 30000)
})

### get_gene_model
species <- "human"
values <- c("1", "2", "3")
sample_df <- data.frame(sample = values)
source_name <- "ensembl_gene_id"
target_name <- "hgnc_symbol"

hgnc_symbols <- c("BRCA1", "TP53", "E2F1")
ensembl_ids <- c("ENSG00000012048", "ENSG00000141510", "ENSG00000101412")
rownames(sample_df) <- ensembl_ids

test_that("get_gene_model stops on bad species", {
  expect_error(emRNASeq::get_gene_model(sample_df, "asd",  source_name,  target_name))
})

test_that("get_gene_model stops on bad namespace", {
  expect_error(emRNASeq::get_gene_model(sample_df, species,  source_name,  "hgnc_symbols"))
  expect_error(emRNASeq::get_gene_model(sample_df, species,  "sensembl_gene_id",  target_name))
})

gene_model <- emRNASeq::get_gene_model(sample_df, species, source_name,  target_name)

test_that("get_gene_model produes a GRanges", {
  expect_is(gene_model, "GRanges")
})

test_that("get_gene_model sets the correct metadata columns", {
  expect_equal(names(GenomicRanges::mcols(gene_model)), c(source_name))
})

test_that("get_gene_model sets the correct names", {
  expect_equal(length(gene_model), length(values))
})