inst/tests/test.detectGenes.R

In monocle: Clustering, differential expression, and trajectory analysis for single- cell RNA-Seq

library(monocle)
library(HSMMSingleCell)
context("detectGenes functions properly 1")


#write test code for this: 

test_that("test detectGenes works properly", {
  data(HSMM_expr_matrix)
  data(HSMM_gene_annotation)
  data(HSMM_sample_sheet)
  pd <- new("AnnotatedDataFrame", data = HSMM_sample_sheet)
  fd <- new("AnnotatedDataFrame", data = HSMM_gene_annotation)
  HSMM <- newCellDataSet(as.matrix(HSMM_expr_matrix), phenoData = pd, featureData = fd)
  
  HSMM <- estimateSizeFactors(HSMM)
  HSMM <- estimateDispersions(HSMM)
  
  expect_error(detectGenes(HSMM), NA)
})