tests/testthat/test_projectR.R

In projectR: Functions for the projection of weights from PCA, CoGAPS, NMF, correlation, and clustering

context("projectR")

test_that("data is proper",{

	expect_that(p.ESepiGen4c1l$mRNA.Seq,is_a('matrix'))
	expect_that(p.ESepiGen4c1l, is_a('list'))
	expect_that(length(p.ESepiGen4c1l),equals(6))
	expect_that(map.ESepiGen4c1l, is_a('data.frame'))
	expect_that(all(dim(map.ESepiGen4c1l) == c(93,9)),is_true())
	expect_that(map.ESepiGen4c1l$GeneSymbols, is_a('character'))
	expect_that(AP.RNAseq6l3c3t, is_a(c('list','CoGAPS')))
	expect_that(length(AP.RNAseq6l3c3t),equals(12))
	expect_that(AP.RNAseq6l3c3t$Amean, is_a('matrix'))
	expect_that(all(dim(AP.RNAseq6l3c3t$Amean) == c(108,5)),is_true())
	expect_that(pd.ESepiGen4c1l,is_a('data.frame'))
	expect_that(all(dim(pd.ESepiGen4c1l) == c(9,2)),is_true())
	expect_that(pd.RNAseq6l3c3t,is_a('data.frame'))
	expect_that(all(dim(pd.RNAseq6l3c3t) == c(54,38)),is_true())
	})

test_that("results are as expected",{
	#CoGAPS check
	library("CoGAPS")
	CR.RNAseq6l3c3t <- CoGAPS(p.RNAseq6l3c3t, params = new("CogapsParams",
nPatterns=5))
	pr_cgps <- projectR(data=p.ESepiGen4c1l$mRNA.Seq,loadings=CR.RNAseq6l3c3t,
		dataNames=map.ESepiGen4c1l[["GeneSymbols"]])
	expect_that(pr_cgps, is_a('matrix'))
	expect_that(all(dim(pr_cgps) == c(5,9)),is_true())
	expect_that(all(pr_cgps != 0), is_true())
	expect_that(all(!is.na(pr_cgps)),is_true())


	#cluster2patter check
	k.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,
		loadings=kmeans(p.RNAseq6l3c3t, 4),
		dataNames=map.ESepiGen4c1l$GeneSymbols,
		loadingsNames=rownames(p.RNAseq6l3c3t),
		full=FALSE, sourceData=p.RNAseq6l3c3t)
	expect_that(all(dim(k.ESepiGen4c1l) == c(4,9)),is_true())
	expect_that(all(k.ESepiGen4c1l != 0), is_true())
	expect_that(all(!is.na(k.ESepiGen4c1l)),is_true())

	#pclust check
	pca.RNAseq6l3c3t<-prcomp(t(p.RNAseq6l3c3t))
	pca.ESepiGen4c1l<-projectR(data=p.ESepiGen4c1l$mRNA.Seq,
		loadings=pca.RNAseq6l3c3t,dataNames=map.ESepiGen4c1l[["GeneSymbols"]])
	expect_that(all(dim(pca.ESepiGen4c1l) == c(54,9)),is_true())
	expect_that(all(pca.ESepiGen4c1l != 0), is_true())
	expect_that(all(!is.na(pca.ESepiGen4c1l)),is_true())
	})