tests/testthat/test-get_indel_context.R

In UMCUGenetics/MutationalPatterns: Comprehensive genome-wide analysis of mutational processes

context("test-get_indel_context")

## Get a GRangesList object with only indels.
indel_grl <- readRDS(system.file("states/blood_grl_indel.rds",
  package = "MutationalPatterns"
))

## Load the corresponding reference genome.
ref_genome <- "BSgenome.Hsapiens.UCSC.hg19"
library(ref_genome, character.only = TRUE)

## Get the indel contexts
output <- get_indel_context(indel_grl, ref_genome)

expected <- readRDS(system.file("states/blood_grl_indel_context.rds",
  package = "MutationalPatterns"
))

test_that("Output has correct class", {
  expect_true(inherits(output, c("GRanges", "CompressedGRangesList")))
})

test_that("Output is equal to expected", {
  expect_equal(output, expected)
})