tests/testthat/test_SL_detect.R

In TomKellyGenetics/slipt: Synthetic Lethal Interaction Prediction Tool (SLIPT) from Cancer Genomics Data

library(slipt)
context("SL detect")

#example data
data <- c()
for(i in 1:100){
  data <- cbind(data, rnorm(1000))
}
rm(i)
rownames(data) <- paste("gene", 1:1000)
colnames(data) <- paste("sample", 1:100)
dim(data)

#load package functions
library("slipt")

##run examples
#partition data
partitioned_data <- prep_data_for_SL(data)
dim(partitioned_data)

test_that("SL predicted for expression quantiles", {
  #load("data/partitioned_data.rda")
  sl_table <- detect_SL("gene 1", partitioned_data)
  dim(sl_table)
  expect_that(dim(sl_table), equals(c(ncol(partitioned_data), 17)))
  expect_that(sl_table[1,1], equals("gene 1"))
  expect_that(!is.na(as.numeric(sl_table[,17])), all)
})

test_that("SL predicted with data preparation", {
  #load("data/data.rda")
  sl_table <- detect_SL("gene 1", prep_data_for_SL(data))
  dim(sl_table)
  expect_that(dim(sl_table), equals(c(ncol(partitioned_data), 17)))
  expect_that(sl_table[1,1], equals("gene 1"))
  expect_that(!is.na(as.numeric(sl_table[,17])), all)
})