tests/testthat/test_pca2go.R

In pcaExplorer: Interactive Visualization of RNA-seq Data Using a Principal Components Approach

library(pcaExplorer)

context("Checks on the functional enrichment of subset of genes/genes with hi loadings")

# testing this is quite lengthy... explore other possibilities?
library(airway)
library(DESeq2)
data(airway)
airway
dds_airway <- DESeqDataSet(airway, design = ~ cell + dex)

# Example, performing extraction of enriched functional categories in
# detected significantly expressed genes
dds_airway <- DESeq(dds_airway)
res_airway <- results(dds_airway)
library("AnnotationDbi")
library("org.Hs.eg.db")
res_airway$symbol <- mapIds(org.Hs.eg.db,
                            keys = row.names(res_airway),
                            column = "SYMBOL",
                            keytype = "ENSEMBL",
                            multiVals = "first")
res_airway$entrez <- mapIds(org.Hs.eg.db,
                            keys = row.names(res_airway),
                            column = "ENTREZID",
                            keytype = "ENSEMBL",
                            multiVals = "first")
expect_is(res_airway, "DESeqResults")
resOrdered <- as.data.frame(res_airway[order(res_airway$padj), ])
de_df <- resOrdered[resOrdered$padj < .05 & !is.na(resOrdered$padj), ]
de_symbols <- de_df$symbol
bg_ids <- rownames(dds_airway)[rowSums(counts(dds_airway)) > 0]
bg_symbols <- mapIds(org.Hs.eg.db,
                     keys = bg_ids,
                     column = "SYMBOL",
                     keytype = "ENSEMBL",
                     multiVals = "first")
library(topGO)

expect_is(de_symbols, "character")
expect_is(bg_symbols, "character")

# topgoDE_airway <- topGOtable(de_symbols, bg_symbols,
#                              ontology = "BP",
#                              mapping = "org.Hs.eg.db",
#                              geneID = "symbol")
#
# expect_is(topgoDE_airway,"data.frame")


rld_airway <- rlogTransformation(dds_airway)

ngenes_pca <- 10000

# goquick_airway <- limmaquickpca2go(rld_airway,
#                                    pca_ngenes = ngenes_pca,
#                                    inputType = "ENSEMBL",
#                                    organism = "Hs")

expect_error(limmaquickpca2go(rld_airway,
                              pca_ngenes = ngenes_pca,
                              inputType = "ENSEMBL",
                              organism = "foo")) # additionally throws a warning

# expect_is(goquick_airway, "list")
# expect_equal(length(goquick_airway), 4) # ensure all pcs are there
# sapply(goquick_airway, names)
#
# expect_equal(attr(goquick_airway, "n_genesforpca"), ngenes_pca)