# Creates the files to be reloaded by the tests for comparisons
library(zeallot)
outputTestDatasetCreation <- function(testsDir = file.path("tests",
"testthat")) {
utils::data("test.dataset", package = "COTAN")
options(parallelly.fork.enable = TRUE)
obj <- COTAN(raw = test.dataset)
obj <- initializeMetaDataset(obj, GEO = " ",
sequencingMethod = "artificial",
sampleCondition = "test")
obj <- proceedToCoex(obj, cores = 6L, saveObj = FALSE)
#saveRDS(obj, file = file.path(testsDir,"temp.RDS"))
cells.names.test <- getCells(obj)[c(1L:10L, 591L:610L, 991L:1000L)]
genes.names.test <- getGenes(obj)[c(1L:10L, 291L:310L, 591L: 600L)]
saveRDS(cells.names.test, file.path(testsDir, "cells.names.test.RDS"))
saveRDS(genes.names.test, file.path(testsDir, "genes.names.test.RDS"))
dispersion.test <- getDispersion(obj)[genes.names.test]
saveRDS(dispersion.test, file.path(testsDir, "dispersion.test.RDS"))
raw.norm.test <- getNuNormData(obj)[genes.names.test, cells.names.test]
saveRDS(raw.norm.test, file.path(testsDir, "raw.norm.test.RDS"))
coex.test <- getGenesCoex(obj, genes = genes.names.test, zeroDiagonal = FALSE)
saveRDS(coex.test, file.path(testsDir, "coex.test.RDS"))
lambda.test <- getLambda(obj)[genes.names.test]
saveRDS(lambda.test, file.path(testsDir, "lambda.test.RDS"))
GDI.test <- calculateGDI(obj)
GDI.test <- GDI.test[genes.names.test, ]
saveRDS(GDI.test, file.path(testsDir, "GDI.test.RDS"))
nu.test <- getNu(obj)[cells.names.test]
saveRDS(nu.test, file.path(testsDir, "nu.test.RDS"))
pval.test <- calculatePValue(obj, geneSubsetCol = genes.names.test)
saveRDS(pval.test, file.path(testsDir, "pval.test.RDS"))
GDIThreshold <- 1.46
ratioAboveThreshold <- 0.01
initialResolution <- 0.8
clusters <- cellsUniformClustering(obj, GDIThreshold = GDIThreshold,
ratioAboveThreshold = ratioAboveThreshold,
initialResolution = initialResolution,
cores = 6L, saveObj = FALSE)[["clusters"]]
saveRDS(clusters, file.path(testsDir, "clusters1.RDS"))
coexDF <- DEAOnClusters(obj, clusters = clusters)
obj <- addClusterization(obj, clName = "clusters",
clusters = clusters, coexDF = coexDF)
saveRDS(coexDF[genes.names.test, ],
file.path(testsDir, "coex.test.cluster1.RDS"))
pvalDF <- pValueFromDEA(coexDF, getNumCells(obj), adjustmentMethod = "none")
saveRDS(pvalDF[genes.names.test, ],
file.path(testsDir, "pval.test.cluster1.RDS"))
c(mergedClusters, mCoexDF) %<-%
mergeUniformCellsClusters(objCOTAN = obj,
clusters = NULL,
GDIThreshold = GDIThreshold,
cores = 6L,
distance = "cosine",
hclustMethod = "ward.D2",
saveObj = FALSE)
saveRDS(mergedClusters[genes.names.test],
file.path(testsDir, "cluster_data_merged.RDS"))
}
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