tests/testthat/test_summarizeExperiment.R
In fmicompbio/mutscan: Preprocessing and Analysis of Deep Mutational Scanning Data
Ldef <- list(
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SUCV", elementsReverse = "SUCV",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 8, 20, 96),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAAAAAGGAAGCTGGAGAGA",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 1,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
collapseToWTForward = FALSE,
collapseToWTReverse = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
maxNReads = -1, verbose = FALSE
)
Ldef1 <- c(
list(fastqForward = system.file("extdata/transInput_1.fastq.gz", package = "mutscan"),
fastqReverse = system.file("extdata/transInput_2.fastq.gz", package = "mutscan")
), Ldef)
Ldef2 <- c(
list(fastqForward = system.file("extdata/transOutput_1.fastq.gz", package = "mutscan"),
fastqReverse = system.file("extdata/transOutput_2.fastq.gz", package = "mutscan")
), Ldef)
out1 <- do.call(digestFastqs, Ldef1)
out2 <- do.call(digestFastqs, Ldef2)
coldata <- data.frame(Name = c("sample1", "sample2"),
Condition = c("input", "output"),
Replicate = c(1, 1), OD = c(0.05, 1.5),
stringsAsFactors = FALSE)
test_that("summarizeExperiment fails with incorrect arguments", {
## x must be a named list, with names matching coldata$Name
expect_error(summarizeExperiment(x = 1, coldata = coldata))
expect_error(summarizeExperiment(x = list(out1), coldata = coldata))
expect_error(summarizeExperiment(x = out1, coldata = coldata))
expect_error(summarizeExperiment(x = list(s1 = out1, s1 = out2), coldata = coldata))
## coldata must be a data.frame with a column Name
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = 1))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata[, c("Condition", "OD")]))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = as.list(coldata)))
## countType must be reads or umis
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = 1))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umi"))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = c("reads", "umis")))
## names must match
expect_error(summarizeExperiment(x = list(s1 = out1, s2 = out2),
coldata = coldata, countType = "umis"))
expect_warning(summarizeExperiment(x = list(sample1 = out1, sample2 = out2,
sample3 = out1),
coldata = coldata, countType = "umis"))
## samples must have the same mutNameDelimiter
tmpout2 <- out2
tmpout2$parameters$mutNameDelimiter <- ":"
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = tmpout2),
coldata = coldata, countType = "reads"))
})
test_that("summarizeExperiment works as expected with reads output", {
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "reads")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(out1$filterSummary$nbrRetained, out2$filterSummary$nbrRetained),
ignore_attr = TRUE)
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrReads), sum(out2$summaryTable$nbrReads)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
expect_true(all(c("mutantName", "sequence", "nbrMutBases",
"minNbrMutBases", "maxNbrMutBases",
"nbrMutCodons", "minNbrMutCodons", "maxNbrMutCodons",
"nbrMutAAs", "minNbrMutAAs", "maxNbrMutAAs",
"sequenceAA", "mutantNameAA", "mutationTypes",
"varLengths") %in%
colnames(SummarizedExperiment::rowData(se))))
## Check that the number of mutated codons are correct (=equal to the number of
## entries in the mutant name that don't contain WT)
expect_equal(sapply(strsplit(SummarizedExperiment::rowData(se)$mutantName, "_"),
function(w) length(w[!grepl("WT", w)])),
SummarizedExperiment::rowData(se)$minNbrMutCodons, ignore_attr = TRUE)
expect_equal(sapply(strsplit(SummarizedExperiment::rowData(se)$mutantName, "_"),
function(w) length(w[!grepl("WT", w)])),
SummarizedExperiment::rowData(se)$maxNbrMutCodons, ignore_attr = TRUE)
## Check that the number of mutated bases is not larger than 3x the number of mutated codons
expect_true(all(SummarizedExperiment::rowData(se)$maxNbrMutBases <=
3 * SummarizedExperiment::rowData(se)$maxNbrMutCodons))
expect_true(all(SummarizedExperiment::rowData(se)$maxNbrMutAAs <=
SummarizedExperiment::rowData(se)$maxNbrMutCodons))
## variable lengths
expect_equal(SummarizedExperiment::rowData(se)$varLengths,
rep("96_96", nrow(se)), ignore_attr = TRUE)
## All variants with no mutated AAs must have a WT in the name
expect_true(all(grepl("WT", SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$maxNbrMutAAs == 0])))
## No mutation for the complete WT
expect_equal(SummarizedExperiment::rowData(se)["f.0.WT_r.0.WT", ]$mutationTypes, "")
## Mutation types for variants with no mutated AAs, but mutated bases, should be silent
expect_true(all(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$maxNbrMutAAs == 0 & SummarizedExperiment::rowData(se)$maxNbrMutBases > 0] == "silent"))
## check translation
expect_equal(SummarizedExperiment::rowData(se)$sequenceAA[3],
mutscan:::translateString(SummarizedExperiment::rowData(se)$sequence[3]))
## Spot checks
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutBases[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 3) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutCodons[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutAAs[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 1) ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], "f.0.WT_r.13.L") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], "nonsynonymous") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutBases[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutCodons[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutAAs[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 0) ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], "f.0.WT_r.0.WT") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], "silent") ## WT: A
})
test_that("summarizeExperiment works as expected with umis output", {
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umis")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrUmis), sum(out2$summaryTable$nbrUmis)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
})
test_that("summarizeExperiment orders samples equally in count matrix/colData", {
se1 <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umis")
se2 <- summarizeExperiment(x = list(sample2 = out2, sample1 = out1),
coldata = coldata, countType = "umis")
m1 <- se1[, match(coldata$Name, colnames(se1))]
m2 <- se2[rownames(m1), match(coldata$Name, colnames(se2))]
expect_equal(SummarizedExperiment::colData(m1), SummarizedExperiment::colData(m2))
expect_equal(SummarizedExperiment::assay(m1, "counts"),
SummarizedExperiment::assay(m2, "counts"))
})
test_that("summarizeExperiment recognizes the presence of UMI counts correctly", {
L1 <- Ldef1; L1$elementsForward <- "SSCV"; L1$elementsReverse <- "SSCV"
L2 <- Ldef2; L2$elementsForward <- "SSCV"; L2$elementsReverse <- "SSCV"
outl1 <- do.call(digestFastqs, L1)
outl2 <- do.call(digestFastqs, L2)
expect_error(summarizeExperiment(x = list(sample1 = outl1, sample2 = outl2),
coldata = coldata, countType = "umis"))
})
test_that("summarizeExperiment works as expected when collapsing to WT", {
## Also test that errorStatistics is empty if there is no constant sequence
Ldef1$collapseToWTForward <- TRUE
Ldef2$collapseToWTForward <- TRUE
Ldef1$elementsForward = "SUSV"
Ldef1$elementsReverse = "SUSV"
Ldef2$elementsForward = "SUSV"
Ldef2$elementsReverse = "SUSV"
out1 <- do.call(digestFastqs, Ldef1)
out2 <- do.call(digestFastqs, Ldef2)
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "reads")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(out1$filterSummary$nbrRetained, out2$filterSummary$nbrRetained),
ignore_attr = TRUE)
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrReads), sum(out2$summaryTable$nbrReads)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
expect_equal(sum(S4Vectors::metadata(se)$errorStatistics[["sample1"]][, c("nbrMatchForward", "nbrMismatchForward", "nbrMatchReverse", "nbrMismatchReverse")]), 0)
expect_equal(sum(S4Vectors::metadata(se)$errorStatistics[["sample2"]][, c("nbrMatchForward", "nbrMismatchForward", "nbrMatchReverse", "nbrMismatchReverse")]), 0)
expect_true(all(c("mutantName", "sequence", "nbrMutBases",
"minNbrMutBases", "maxNbrMutBases",
"nbrMutCodons", "minNbrMutCodons", "maxNbrMutCodons",
"nbrMutAAs", "minNbrMutAAs", "maxNbrMutAAs",
"sequenceAA", "mutantNameAA", "mutationTypes",
"varLengths") %in%
colnames(SummarizedExperiment::rowData(se))))
## variable lengths
expect_equal(SummarizedExperiment::rowData(se)$varLengths,
rep("96_96", nrow(se)), ignore_attr = TRUE)
expect_false(any(grepl("^,", SummarizedExperiment::rowData(se)$mutationTypes)))
expect_false(any(grepl(",$", SummarizedExperiment::rowData(se)$mutationTypes)))
expect_equal(SummarizedExperiment::rowData(se)$sequenceAA[3],
mutscan:::translateString(SummarizedExperiment::rowData(se)$sequence[3]))
expect_type(SummarizedExperiment::rowData(se)$nbrMutBases, "character")
expect_type(SummarizedExperiment::rowData(se)$nbrMutCodons, "character")
expect_type(SummarizedExperiment::rowData(se)$nbrMutAAs, "character")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutBases[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1,2,3")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutCodons[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutAAs[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1")
expect_true(all(grepl("stop", SummarizedExperiment::rowData(se)$mutationTypes[grep("\\*", SummarizedExperiment::rowData(se)$mutantNameAA)])))
})
test_that("mergeValues works", {
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a,b", "b,c", "c", "b,c", "b,a", "d"))
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a,b,c", "b,c,d", "c", "a,b"))
res <- mergeValues(c("B", "A", "C", "D"),
c("a,b", "c", "c", "d"))
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("c", "a,b", "c", "d"))
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a:b", "b:c", "c", "b:c", "b:a", "d"),
delimiter = ":")
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a:b:c", "b:c:d", "c", "a:b"))
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a,b", "b:c", "c", "b:c", "b:a", "d"),
delimiter = ":")
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a,b:b:c", "b:c:d", "c", "a:b"))
})
fmicompbio/mutscan documentation built on March 30, 2024, 9:13 a.m.
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Ldef <- list(
mergeForwardReverse = FALSE,
minOverlap = 0, maxOverlap = 0, maxFracMismatchOverlap = 0, greedyOverlap = TRUE,
revComplForward = FALSE, revComplReverse = FALSE,
elementsForward = "SUCV", elementsReverse = "SUCV",
elementLengthsForward = c(1, 10, 18, 96),
elementLengthsReverse = c(1, 8, 20, 96),
adapterForward = "GGAAGAGCACACGTC",
adapterReverse = "GGAAGAGCGTCGTGT",
primerForward = "",
primerReverse = "",
wildTypeForward = "ACTGATACACTCCAAGCGGAGACAGACCAACTAGAAGATGAGAAGTCTGCTTTGCAGACCGAGATTGCCAACCTGCTGAAGGAGAAGGAAAAACTA",
wildTypeReverse = "ATCGCCCGGCTGGAGGAAAAAGTGAAAACCTTGAAAGCTCAGAACTCGGAGCTGGCGTCCACGGCCAACATGCTCAGGGAACAGGTGGCACAGCTT",
constantForward = "AACCGGAGGAGGGAGCTG",
constantReverse = "GAAAAAGGAAGCTGGAGAGA",
avePhredMinForward = 20.0, avePhredMinReverse = 20.0,
variableNMaxForward = 0, variableNMaxReverse = 0,
umiNMax = 0,
nbrMutatedCodonsMaxForward = 1,
nbrMutatedCodonsMaxReverse = 1,
nbrMutatedBasesMaxForward = -1,
nbrMutatedBasesMaxReverse = -1,
forbiddenMutatedCodonsForward = "NNW",
forbiddenMutatedCodonsReverse = "NNW",
useTreeWTmatch = FALSE,
collapseToWTForward = FALSE,
collapseToWTReverse = FALSE,
mutatedPhredMinForward = 0.0, mutatedPhredMinReverse = 0.0,
mutNameDelimiter = ".",
constantMaxDistForward = -1,
constantMaxDistReverse = -1,
umiCollapseMaxDist = 0,
maxNReads = -1, verbose = FALSE
)
Ldef1 <- c(
list(fastqForward = system.file("extdata/transInput_1.fastq.gz", package = "mutscan"),
fastqReverse = system.file("extdata/transInput_2.fastq.gz", package = "mutscan")
), Ldef)
Ldef2 <- c(
list(fastqForward = system.file("extdata/transOutput_1.fastq.gz", package = "mutscan"),
fastqReverse = system.file("extdata/transOutput_2.fastq.gz", package = "mutscan")
), Ldef)
out1 <- do.call(digestFastqs, Ldef1)
out2 <- do.call(digestFastqs, Ldef2)
coldata <- data.frame(Name = c("sample1", "sample2"),
Condition = c("input", "output"),
Replicate = c(1, 1), OD = c(0.05, 1.5),
stringsAsFactors = FALSE)
test_that("summarizeExperiment fails with incorrect arguments", {
## x must be a named list, with names matching coldata$Name
expect_error(summarizeExperiment(x = 1, coldata = coldata))
expect_error(summarizeExperiment(x = list(out1), coldata = coldata))
expect_error(summarizeExperiment(x = out1, coldata = coldata))
expect_error(summarizeExperiment(x = list(s1 = out1, s1 = out2), coldata = coldata))
## coldata must be a data.frame with a column Name
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = 1))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata[, c("Condition", "OD")]))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = as.list(coldata)))
## countType must be reads or umis
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = 1))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umi"))
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = c("reads", "umis")))
## names must match
expect_error(summarizeExperiment(x = list(s1 = out1, s2 = out2),
coldata = coldata, countType = "umis"))
expect_warning(summarizeExperiment(x = list(sample1 = out1, sample2 = out2,
sample3 = out1),
coldata = coldata, countType = "umis"))
## samples must have the same mutNameDelimiter
tmpout2 <- out2
tmpout2$parameters$mutNameDelimiter <- ":"
expect_error(summarizeExperiment(x = list(sample1 = out1, sample2 = tmpout2),
coldata = coldata, countType = "reads"))
})
test_that("summarizeExperiment works as expected with reads output", {
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "reads")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(out1$filterSummary$nbrRetained, out2$filterSummary$nbrRetained),
ignore_attr = TRUE)
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrReads), sum(out2$summaryTable$nbrReads)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
expect_true(all(c("mutantName", "sequence", "nbrMutBases",
"minNbrMutBases", "maxNbrMutBases",
"nbrMutCodons", "minNbrMutCodons", "maxNbrMutCodons",
"nbrMutAAs", "minNbrMutAAs", "maxNbrMutAAs",
"sequenceAA", "mutantNameAA", "mutationTypes",
"varLengths") %in%
colnames(SummarizedExperiment::rowData(se))))
## Check that the number of mutated codons are correct (=equal to the number of
## entries in the mutant name that don't contain WT)
expect_equal(sapply(strsplit(SummarizedExperiment::rowData(se)$mutantName, "_"),
function(w) length(w[!grepl("WT", w)])),
SummarizedExperiment::rowData(se)$minNbrMutCodons, ignore_attr = TRUE)
expect_equal(sapply(strsplit(SummarizedExperiment::rowData(se)$mutantName, "_"),
function(w) length(w[!grepl("WT", w)])),
SummarizedExperiment::rowData(se)$maxNbrMutCodons, ignore_attr = TRUE)
## Check that the number of mutated bases is not larger than 3x the number of mutated codons
expect_true(all(SummarizedExperiment::rowData(se)$maxNbrMutBases <=
3 * SummarizedExperiment::rowData(se)$maxNbrMutCodons))
expect_true(all(SummarizedExperiment::rowData(se)$maxNbrMutAAs <=
SummarizedExperiment::rowData(se)$maxNbrMutCodons))
## variable lengths
expect_equal(SummarizedExperiment::rowData(se)$varLengths,
rep("96_96", nrow(se)), ignore_attr = TRUE)
## All variants with no mutated AAs must have a WT in the name
expect_true(all(grepl("WT", SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$maxNbrMutAAs == 0])))
## No mutation for the complete WT
expect_equal(SummarizedExperiment::rowData(se)["f.0.WT_r.0.WT", ]$mutationTypes, "")
## Mutation types for variants with no mutated AAs, but mutated bases, should be silent
expect_true(all(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$maxNbrMutAAs == 0 & SummarizedExperiment::rowData(se)$maxNbrMutBases > 0] == "silent"))
## check translation
expect_equal(SummarizedExperiment::rowData(se)$sequenceAA[3],
mutscan:::translateString(SummarizedExperiment::rowData(se)$sequence[3]))
## Spot checks
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutBases[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 3) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutCodons[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutAAs[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], 1) ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], "f.0.WT_r.13.L") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.CTC"], "nonsynonymous") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutBases[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutCodons[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 1) ## WT: GCT
expect_equal(SummarizedExperiment::rowData(se)$minNbrMutAAs[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], 0) ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutantNameAA[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], "f.0.WT_r.0.WT") ## WT: A
expect_equal(SummarizedExperiment::rowData(se)$mutationTypes[SummarizedExperiment::rowData(se)$mutantName == "f.0.WT_r.13.GCG"], "silent") ## WT: A
})
test_that("summarizeExperiment works as expected with umis output", {
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umis")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrUmis), sum(out2$summaryTable$nbrUmis)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
})
test_that("summarizeExperiment orders samples equally in count matrix/colData", {
se1 <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "umis")
se2 <- summarizeExperiment(x = list(sample2 = out2, sample1 = out1),
coldata = coldata, countType = "umis")
m1 <- se1[, match(coldata$Name, colnames(se1))]
m2 <- se2[rownames(m1), match(coldata$Name, colnames(se2))]
expect_equal(SummarizedExperiment::colData(m1), SummarizedExperiment::colData(m2))
expect_equal(SummarizedExperiment::assay(m1, "counts"),
SummarizedExperiment::assay(m2, "counts"))
})
test_that("summarizeExperiment recognizes the presence of UMI counts correctly", {
L1 <- Ldef1; L1$elementsForward <- "SSCV"; L1$elementsReverse <- "SSCV"
L2 <- Ldef2; L2$elementsForward <- "SSCV"; L2$elementsReverse <- "SSCV"
outl1 <- do.call(digestFastqs, L1)
outl2 <- do.call(digestFastqs, L2)
expect_error(summarizeExperiment(x = list(sample1 = outl1, sample2 = outl2),
coldata = coldata, countType = "umis"))
})
test_that("summarizeExperiment works as expected when collapsing to WT", {
## Also test that errorStatistics is empty if there is no constant sequence
Ldef1$collapseToWTForward <- TRUE
Ldef2$collapseToWTForward <- TRUE
Ldef1$elementsForward = "SUSV"
Ldef1$elementsReverse = "SUSV"
Ldef2$elementsForward = "SUSV"
Ldef2$elementsReverse = "SUSV"
out1 <- do.call(digestFastqs, Ldef1)
out2 <- do.call(digestFastqs, Ldef2)
se <- summarizeExperiment(x = list(sample1 = out1, sample2 = out2),
coldata = coldata, countType = "reads")
expect_equal(nrow(se), length(union(out1$summaryTable$mutantName,
out2$summaryTable$mutantName)))
expect_equal(ncol(se), 2)
expect_equal(sort(rownames(se)),
sort(union(out1$summaryTable$mutantName, out2$summaryTable$mutantName)))
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(out1$filterSummary$nbrRetained, out2$filterSummary$nbrRetained),
ignore_attr = TRUE)
expect_equal(Matrix::colSums(SummarizedExperiment::assay(se, "counts")),
c(sum(out1$summaryTable$nbrReads), sum(out2$summaryTable$nbrReads)),
ignore_attr = TRUE)
for (cn in colnames(out1$filterSummary)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
out1$filterSummary[, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
out2$filterSummary[, cn])
}
for (cn in colnames(coldata)) {
expect_equal(SummarizedExperiment::colData(se)["sample1", cn],
coldata[1, cn])
expect_equal(SummarizedExperiment::colData(se)["sample2", cn],
coldata[2, cn])
}
expect_equal(S4Vectors::metadata(se)$parameters[["sample1"]], out1$parameters)
expect_equal(S4Vectors::metadata(se)$parameters[["sample2"]], out2$parameters)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample1"]], out1$errorStatistics)
expect_equal(S4Vectors::metadata(se)$errorStatistics[["sample2"]], out2$errorStatistics)
expect_equal(sum(S4Vectors::metadata(se)$errorStatistics[["sample1"]][, c("nbrMatchForward", "nbrMismatchForward", "nbrMatchReverse", "nbrMismatchReverse")]), 0)
expect_equal(sum(S4Vectors::metadata(se)$errorStatistics[["sample2"]][, c("nbrMatchForward", "nbrMismatchForward", "nbrMatchReverse", "nbrMismatchReverse")]), 0)
expect_true(all(c("mutantName", "sequence", "nbrMutBases",
"minNbrMutBases", "maxNbrMutBases",
"nbrMutCodons", "minNbrMutCodons", "maxNbrMutCodons",
"nbrMutAAs", "minNbrMutAAs", "maxNbrMutAAs",
"sequenceAA", "mutantNameAA", "mutationTypes",
"varLengths") %in%
colnames(SummarizedExperiment::rowData(se))))
## variable lengths
expect_equal(SummarizedExperiment::rowData(se)$varLengths,
rep("96_96", nrow(se)), ignore_attr = TRUE)
expect_false(any(grepl("^,", SummarizedExperiment::rowData(se)$mutationTypes)))
expect_false(any(grepl(",$", SummarizedExperiment::rowData(se)$mutationTypes)))
expect_equal(SummarizedExperiment::rowData(se)$sequenceAA[3],
mutscan:::translateString(SummarizedExperiment::rowData(se)$sequence[3]))
expect_type(SummarizedExperiment::rowData(se)$nbrMutBases, "character")
expect_type(SummarizedExperiment::rowData(se)$nbrMutCodons, "character")
expect_type(SummarizedExperiment::rowData(se)$nbrMutAAs, "character")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutBases[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1,2,3")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutCodons[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1")
expect_equal(SummarizedExperiment::rowData(se)$nbrMutAAs[[which(SummarizedExperiment::rowData(se)$mutantName == "f_r.0.WT")]], "0,1")
expect_true(all(grepl("stop", SummarizedExperiment::rowData(se)$mutationTypes[grep("\\*", SummarizedExperiment::rowData(se)$mutantNameAA)])))
})
test_that("mergeValues works", {
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a,b", "b,c", "c", "b,c", "b,a", "d"))
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a,b,c", "b,c,d", "c", "a,b"))
res <- mergeValues(c("B", "A", "C", "D"),
c("a,b", "c", "c", "d"))
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("c", "a,b", "c", "d"))
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a:b", "b:c", "c", "b:c", "b:a", "d"),
delimiter = ":")
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a:b:c", "b:c:d", "c", "a:b"))
res <- mergeValues(c("A", "B", "C", "A", "D", "B"),
c("a,b", "b:c", "c", "b:c", "b:a", "d"),
delimiter = ":")
expect_s3_class(res, "data.frame")
expect_named(res, c("mutantNameColl", "valueColl"))
expect_equal(res$mutantNameColl, c("A", "B", "C", "D"))
expect_equal(res$value, c("a,b:b:c", "b:c:d", "c", "a:b"))
})
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