tests/testthat/testPSIquantification.R

In nuno-agostinho/psichomics: Graphical Interface for Alternative Splicing Quantification, Analysis and Visualisation

context("Calculate inclusion levels")

test_that("createJunctionsTemplate creates a template of junctions with NAs", {
    nrow <- 8
    temp <- createJunctionsTemplate(nrow)
    expect_equal(nrow(temp), nrow)
    expect_true(all(is.na(temp)))
    coords <- c("C1.start", "C1.end", "A1.start", "A1.end",
                "A2.start", "A2.end", "C2.start", "C2.end")
    expect_equal(names(temp), coords)
    
    nrow <- 2
    temp <- createJunctionsTemplate(nrow, program="MISO",
                                    event.type=c("A5SS", "SE"), 
                                    chromosome=c(2, 4),
                                    strand=c("-", "+"))
    expect_equal(nrow(temp), nrow)
    expect_false(all(is.na(temp)))
    expect_equal(names(temp), c(coords, "Program", "Event.type", "Chromosome", 
                                "Strand"))
    expect_equal(temp$Program, c("MISO", "MISO"))
    expect_equal(temp$Event.type, c("A5SS", "SE"))
    expect_equal(temp$Chromosome, c(2, 4))
    expect_equal(temp$Strand, c("-", "+"))
})

test_that("Calculate inclusion levels for exon skipping", {
    library(fastmatch)
    
    eventType <- "SE"
    annot <- readFile("ex_splicing_annotation.RDS")$`Skipped exon`
    junctionQuant <- as.matrix(readFile("ex_junctionQuant.RDS"))
    psi <- calculateInclusionLevels(eventType, junctionQuant, annot)
    
    expect_true(all(psi[1, ] == 0.5)) # Same reads for all junctions
    expect_true(all(psi[2, ] > 0.5)) # More reads for inclusion isoform
    expect_true(all(psi[3, c(1, 3:5)] < 0.5)) # More reads for exclusive isoform
})

test_that("Calculate inclusion levels for exon skipping with minimum reads", {
    library(fastmatch)
    
    eventType <- "SE"
    minReads <- 15
    annot <- readFile("ex_splicing_annotation.RDS")$`Skipped exon`
    
    junctionQuant <- read.table(text = "1 1 1 1 1 1
                                1 1 1 1 1 1
                                1 1 1 1 1 1
                                27 20 90 24 1 35
                                10 18 13 12 1 21
                                30 24 92 26 1 29
                                27 20 90 24 14 35
                                90 98 93 92 90 91
                                30 24 92 26 13 29")
    junctionQuant <- as.matrix(junctionQuant)
    names(junctionQuant) <- c(paste("Normal", 1:3), paste("Cancer", 1:3))
    rownames(junctionQuant) <- c("chr1:32:35:+",
                                 "chr1:32:38:+",
                                 "chr1:37:38:+",
                                 "chr2:32:35:+",
                                 "chr2:32:38:+",
                                 "chr2:37:38:+",
                                 "chr3:32:35:+",
                                 "chr3:32:38:+",
                                 "chr3:37:38:+")
    psi <- calculateInclusionLevels(eventType, junctionQuant, annot, minReads)
    
    expect_equal(nrow(psi), 2) # Discard first event based on few reads
    expect_true(is.na(psi[1, 5]))
    expect_true(all(psi[1, -5] > 0.5)) # More reads for inclusion isoform
    expect_true(all(psi[2, ] < 0.5)) # More reads for exclusive isoform
})

test_that("Calculate inclusion levels for mutually exclusive exons", {
    library(fastmatch)
    
    eventType <- "MXE"
    annot <- readFile("ex_splicing_annotation.RDS")$`Mutually exclusive exon`
    junctionQuant <- as.matrix(readFile("ex_junctionQuant.RDS"))
    psi <- calculateInclusionLevels(eventType, junctionQuant, annot)
    
    expect_true(all(psi[1, ] == 0.5)) # Same reads for all junctions
    expect_true(all(psi[2, ] > 0.5)) # More reads for inclusive isoform
    expect_true(all(psi[3, ] < 0.5)) # More reads for exclusive isoform
})

test_that("Calculate inclusion levels for alternative 5' splice site", {
    library(fastmatch)
    
    eventType <- "A5SS"
    annot <- read.table(text = "1 + 32 35 37
                        2 + 32 35 37
                        3 + 32 35 37")
    names(annot) <- c("Chromosome", "Strand", "Constitutive exon 1 end",
                      "Alternative exon 1 end", "Constitutive exon 2 start")
    junctionQuant <- read.table(text = "10 10 10 10 10 10
                                10 10 10 10 10 10
                                10 14 12 16 13 19
                                27 20 90 24 14 35
                                30 24 92 26 13 29
                                10 18 13 12 10 21")
    names(junctionQuant) <- c(paste("Normal", 1:3), paste("Cancer", 1:3))
    rownames(junctionQuant) <- c("chr1:32:37:+",
                                 "chr1:35:37:+",
                                 "chr2:32:37:+",
                                 "chr2:35:37:+",
                                 "chr3:32:37:+",
                                 "chr3:35:37:+")
    junctionQuant <- as.matrix(junctionQuant)
    psi <- calculateInclusionLevels(eventType, junctionQuant, annot)
    
    expect_true(all(psi[1, ] == 0.5)) # Same reads for all junctions
    expect_true(all(psi[2, ] > 0.5)) # More reads for inclusive isoform
    expect_true(all(psi[3, ] < 0.5)) # More reads for exclusive isoform
})

test_that("Calculate inclusion levels for alternative 3' splice site", {
    library(fastmatch)
    
    eventType <- "A3SS"
    annot <- read.table(text = "1 + 32 35 37
                        2 + 32 35 37
                        3 + 32 35 37")
    names(annot) <- c("Chromosome", "Strand", "Constitutive exon 1 end", 
                      "Alternative exon 1 start", "Constitutive exon 2 start")
    junctionQuant <- read.table(text = "10 10 10 10 10 10
                                10 10 10 10 10 10
                                27 20 90 24 14 35
                                10 14 12 16 13 19
                                10 18 13 12 10 21
                                30 24 92 26 13 29")
    names(junctionQuant) <- c(paste("Normal", 1:3), paste("Cancer", 1:3))
    rownames(junctionQuant) <- c("chr1:32:35:+",
                                 "chr1:32:37:+",
                                 "chr2:32:35:+",
                                 "chr2:32:37:+",
                                 "chr3:32:35:+",
                                 "chr3:32:37:+")
    junctionQuant <- as.matrix(junctionQuant)
    psi <- calculateInclusionLevels(eventType, junctionQuant, annot)
    
    expect_true(all(psi[1, ] == 0.5)) # Same reads for all junctions
    expect_true(all(psi[2, ] > 0.5)) # More reads for inclusive isoform
    expect_true(all(psi[3, ] < 0.5)) # More reads for exclusive isoform
})

test_that("Process splicing quantification for multiple event types", {
    eventType <- c("SE", "MXE")
    annot <- readFile("ex_splicing_annotation.RDS")
    junctionQuant <- readFile("ex_junctionQuant.RDS")
    psi <- quantifySplicing(annot, junctionQuant, eventType=c("SE", "MXE"))
    expect_is(psi, "data.frame")
    
    expect_equal(nrow(psi), 6)
    expect_length(grep("SE_[1-3]", rownames(psi)), 3)
    expect_length(grep("MXE_[1-3]", rownames(psi)), 3)
    
    expect_equal(colnames(psi), colnames(junctionQuant))
    expect_equal(attr(psi, "dataType"), "Inclusion levels")
    
    # The portion with just the skipped exon should be the same as a subset
    # when calculating for more event types
    junctionQuant <- as.matrix(junctionQuant)
    psiSE <- quantifySplicing(annot, junctionQuant, eventType="SE")
    expect_equivalent(psi[1:3, ], psiSE)
})