tests/testthat/test.estimateDispersions.R

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

library(HSMMSingleCell)
library(monocle)
library(dplyr)
context("estimateDispersions")


test_that("estimateDispersion() properly validates its input",{
  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,
                         lowerDetectionLimit=1,
                         expressionFamily=tobit())
  HSMM <- estimateSizeFactors(HSMM)
  expect_error(estimateDispersions(HSMM))
  
  
  
  lung <- load_lung()
  lung_pData <- pData(lung)
  expect_equal(colnames(lung_pData), c("file", "total_mass", "internal_scale", "external_scale","median_transcript_frags", "BioSample", "age", "genotype", "Sample.Name", "SRA.Sample", "MBases", "MBytes", "SRA.Study", "BioProject", "source_name", "strain", "tissue", "Assay.Type", "Center.Name", 
                                      "Platform", "Consent", "Time", "Size_Factor", "Total_mRNAs", "endogenous_RNA", "Pseudotime", "State", "Parent", "num_genes_expressed"))
  expect_true(all(lung_pData$total_mass >= 392))
  expect_true(all(lung_pData$total_mass <= 4086580))
  expect_true(all(lung_pData$internal_scale >= 0.00153031))
  expect_true(all(lung_pData$internal_scale <= 11.0584))
  expect_true(all(lung_pData$external_scale == 1))
  expect_true(all(lung_pData$median_transcript_frags >= 1.03129e-06))
  expect_true(all(lung_pData$median_transcript_frags <= 3.48372))
  expect_true(all(substring(lung_pData$BioSample, 0, 5) == "SAMN0"))
  expect_equal(levels(lung_pData$age), c("Embryonic day 14.5", "Embryonic day 16.5", "Embryonic day 18.5", "post natal day 107"))
  expect_equal(levels(lung_pData$genotype), c("Sftpc-Cre-ERT2-rtta -/- tetO-HIST1H2BJ-GFP+/-)", "wild type"))
  expect_true(all(substring(lung_pData$Sample.Name, 0, 6) == "GSM127"))
  expect_equal(substring(lung_pData$Sample.Name[1], 7, 10), "1863")
  expect_equal(substring(lung_pData$Sample.Name[185], 7, 10), "2062")
  expect_equal(toString(lung_pData$SRA.Sample[1]), "SRS504890")
  expect_equal(toString(lung_pData$SRA.Sample[185]), "SRS505090")
  expect_true(all(lung_pData$MBases >= 0))
  expect_true(all(lung_pData$MBases <= 961))
  expect_true(all(lung_pData$MBytes >= 0))
  expect_true(all(lung_pData$MBases <= 1000))
  expect_equal(levels(lung_pData$SRA.Study), "SRP033209")
  expect_equal(levels(lung_pData$BioProject), "GSE52583")
  expect_equal(levels(lung_pData$source_name), "distal lung epithelium")
  expect_equal(levels(lung_pData$strain), "C57BL/6J")
  expect_equal(levels(lung_pData$tissue), "lung")
  expect_equal(levels(lung_pData$Assay.Type), "RNA-Seq")
  expect_equal(levels(lung_pData$Center.Name), "GEO")
  expect_equal(levels(lung_pData$Platform), "ILLUMINA")
  expect_equal(levels(lung_pData$Consent), "public")
  expect_true(all(lung_pData$Size_Factor >= 0.2896533))
  expect_true(all(lung_pData$Size_Factor <= 4.08098))
  expect_true(all(lung_pData$Total_mRNAs >= 50.43858))
  expect_true(all(lung_pData$Total_mRNAs <= 16184.72))
  expect_true(all(lung_pData$endogenous_RNA >= 251.1154))
  expect_true(all(lung_pData$endogenous_RNA <= 194030))
  expect_true(all(lung_pData$Pseudotime >= 0))
  expect_true(all(lung_pData$Pseudotime <= 16.67064))
  expect_equal(levels(lung_pData$State), c("1", "2", "3"))
  expect_true((is.na(substring(lung_pData$Parent, 0, 6)) || substring(lung_pData$Parent, 0, 6) == "SRR103"))
  expect_true(all(lung_pData$num_genes_expressed >= 10))
  expect_true(all(lung_pData$num_genes_expressed <= 196)) 
})