tests/testthat/test_005_annotation_biomart.R

In elsayed-lab/hpgltools: A pile of (hopefully) useful R functions

start <- as.POSIXlt(Sys.time())
context("005annotation_biomart.R")
## 2017-12, exported functions in annotation_biomart:
##   load_biomart_annotations(), load_biomart_go(), load_biomart_orthologs()

testing <- load_biomart_annotations(species = "hsapiens", overwrite=TRUE,
                                    year = "2020", month = "jan")
annotations <- testing[["annotation"]]
gene_ids <- head(sort(annotations[["ensembl_transcript_id"]]))
expected <- c("ENST00000000233", "ENST00000000412", "ENST00000000442",
              "ENST00000001008", "ENST00000001146", "ENST00000002125")
## 01
test_that("Do we get expected gene IDs?", {
  expect_equal(expected, gene_ids)
})

data <- testing[["annotation"]]
expected <- 200000
actual <- nrow(data)
## 02
test_that("Do we receive expected output from load_biomart_annotations()?", {
  expect_gt(actual, expected)
})

## load_biomart_go()
testing <- load_biomart_go(species = "hsapiens", overwrite = TRUE)
data <- testing[["go"]]
expected <- 40000
actual <- nrow(data)
## 03
test_that("Do we receive expected output from load_biomart_go()?", {
  expect_gt(actual, expected)
})

## load_biomart_orthologs()
## I should probably set this to an explicit revision of biomart.
testing <- load_biomart_orthologs(gene_ids = gene_ids, first_species = "hsapiens",
                                  second_species = "mmusculus", year = 2020,
                                  month = "jan")
data <- testing[["all_linked_genes"]]
actual <- nrow(data)
expected <- 23000
## 04
test_that("Do we get expected orthologs from load_biomart_orthologs()?", {
  expect_gt(actual, expected)
})

end <- as.POSIXlt(Sys.time())
elapsed <- round(x = as.numeric(end - start))
message("\nFinished 005annotation_biomart.R in ", elapsed,  " seconds.")