inst/unitTests/test_combine-methods.R
In Bioconductor/SummarizedExperiment: A container (S4 class) for matrix-like assays
test_combineRows_unnamed <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10),
normalized=matrix(rnorm(1000), ncol=10)))
colData(se2)$B <- 2
rowData(se2)$B <- "B"
stuff <- combineRows(se, se2, use.names=FALSE)
# Column data is correctly combined.
checkIdentical(stuff$A, rep(1, ncol(stuff)))
checkIdentical(stuff$B, rep(2, ncol(stuff)))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), nrow(se2))))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(nrow(se), nrow(se2))))
# Assay data is correctly combined.
checkIdentical(as.matrix(assay(stuff)), rbind(assay(se), assay(se2)))
checkIdentical(as.matrix(assay(stuff, 2)), rbind(matrix(NA, nrow(se), ncol(se)), assay(se2, 2)))
# Unary methods work as expected.
checkIdentical(se, combineRows(se, delayed=FALSE, use.names=FALSE))
}
test_combineRows_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=20),
normalized=matrix(rnorm(1000), ncol=20)))
colData(se2)$B <- 2
rowData(se2)$B <- "B"
# This fails, because we expect matching numbers of columns when use.names=TRUE.
checkException(combineRows(se, se2), silent=TRUE)
colnames(se) <- letters[1:10]
colnames(se2) <- letters[3:22]
stuff <- combineRows(se, se2)
# Column data is correctly combined
checkIdentical(colnames(stuff), letters[1:22])
checkIdentical(stuff$A, rep(c(1, NA), c(ncol(se), 12)))
checkIdentical(stuff$B, rep(c(NA, 2), c(2, ncol(se2))))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), nrow(se2))))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(nrow(se), nrow(se2))))
# Assay data is correctly combined.
mat <- as.matrix(assay(stuff))
ref <- rbind(
cbind(assay(se), matrix(NA, nrow(se), ncol=12)),
cbind(NA, NA, assay(se2))
)
colnames(ref) <- letters[1:22]
checkIdentical(mat, ref)
mat <- as.matrix(assay(stuff, 2))
ref <- rbind(
matrix(NA, nrow(se), ncol(stuff)),
cbind(NA, NA, assay(se2, 2))
)
colnames(ref) <- letters[1:22]
checkIdentical(mat, ref)
# Unary methods work as expected.
checkIdentical(se, combineRows(se, delayed=FALSE))
}
test_combineRows_assays <- function() {
# Deep dive into correct assay name behavior.
se <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10),
matrix(rnorm(1000), ncol=10)))
colnames(se) <- letters[1:10]
colnames(se2) <- letters[15:24]
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# This should fail due to differences in the number of _unnamed_ assays.
checkException(combineRows(se, se2), silent=TRUE)
# Either all assays are named, or all are unnamed.
assays(se) <- assays(se)[c(1, 1)]
assayNames(se2) <- c("WHEE", "BLAH")
checkException(combineRows(se, se2), silent=TRUE)
assays(se2) <- unname(assays(se2))
out <- combineRows(se, se2)
checkIdentical(colnames(out), letters[c(1:10, 15:24)])
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
}
test_combineRows_ranges_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# Returns a vanilla SE.
out <- combineRows(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
# Returns a GRanges.
replace <- GRanges("chrA", IRanges(1, 1:100))
names(replace) <- rownames(se)
rowRanges(se) <- replace
replace2 <- GRanges("chrB", IRanges(1, 1:100))
names(replace2) <- rownames(se2)
rowRanges(se2) <- replace2
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rowRanges(out), suppressWarnings(c(replace, replace2)))
# Testing different objects.
se3 <- se2
rowRanges(se3) <- NULL
rownames(se3) <- rownames(se2)
suppressWarnings(out <- combineRows(se, se3, use.names=FALSE))
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(c(1L, 0L), c(nrow(se), nrow(se3))))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineRows(se, se4, use.names=FALSE))
expected <- suppressWarnings(as(c(replace, replace2), "GRangesList"))
checkIdentical(rowRanges(out), expected)
# Order doesn't affect conversion to GRL.
suppressWarnings(out <- combineRows(se4, se, use.names=FALSE))
expected <- suppressWarnings(as(c(replace2, replace), "GRangesList"))
checkIdentical(rowRanges(out), expected)
suppressWarnings(combined <- rowRanges(combineRows(se, se3, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(1L, 0L, 1L), c(nrow(se), nrow(se3), nrow(se4))))
suppressWarnings(combined <- rowRanges(combineRows(se3, se, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(0L, 1L, 1L), c(nrow(se3), nrow(se), nrow(se4))))
}
test_combineRows_ranges_unnamed <- function() {
# Repeating the same suite of tests for SEs without rownames.
# This checks the correctness of some edge-case behaviors.
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
# Returns a vanilla SE.
out <- combineRows(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(nrow(out), nrow(se) + nrow(se2))
# Returns a GRanges.
rowRanges(se) <- GRanges("chrA", IRanges(1, 1:100))
rowRanges(se2) <- GRanges("chrB", IRanges(1, 1:100))
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rowRanges(out), suppressWarnings(c(rowRanges(se), rowRanges(se2))))
# Testing different objects.
se3 <- se2
rowRanges(se3) <- NULL
suppressWarnings(out <- combineRows(se, se3, use.names=FALSE))
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(c(1L, 0L), c(nrow(se), nrow(se3))))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineRows(se, se4, use.names=FALSE))
expected <- suppressWarnings(as(c(rowRanges(se), rowRanges(se2)), "GRangesList"))
checkIdentical(rowRanges(out), expected)
suppressWarnings(combined <- rowRanges(combineRows(se, se3, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(1L, 0L, 1L), c(nrow(se), nrow(se3), nrow(se4))))
# Handles partial row names.
rownames(se) <- paste0("GENE_", 1:100)
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rownames(out), c(rownames(se), character(nrow(se2))))
}
test_combineCols_unnamed <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1L
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10),
normalized=matrix(rnorm(1000), ncol=10)))
colData(se2)$A <- 2L
colData(se2)$B <- 3
rowData(se2)$B <- "B"
stuff <- combineCols(se, se2, use.names=FALSE)
# Column data is correctly combined.
checkIdentical(stuff$A, rep(1:2, each=10))
checkIdentical(stuff$B, rep(c(NA, 3), each=10))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(1, nrow(se)))
checkIdentical(rowData(stuff)$B, rep("B", nrow(se)))
# Assay data is correctly combined.
checkIdentical(as.matrix(assay(stuff)), cbind(assay(se), assay(se2)))
checkIdentical(as.matrix(assay(stuff, 2)), cbind(matrix(NA, nrow(se), ncol(se)), assay(se2, 2)))
# Unary methods work as expected.
checkIdentical(se, combineCols(se, delayed=FALSE, use.names=FALSE))
}
test_combineCols_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=100)))
colData(se)$A <- 1L
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=50),
normalized=matrix(rnorm(1000), ncol=50)))
colData(se2)$A <- 2L
colData(se2)$B <- 3
rowData(se2)$B <- "B"
# This fails, because we expect matching numbers of columns when use.names=TRUE.
checkException(combineCols(se, se2), silent=TRUE)
rownames(se) <- letters[1:10]
rownames(se2) <- letters[3:22]
stuff <- combineCols(se, se2)
# Column data is correctly combined
checkIdentical(rownames(stuff), letters[1:22])
checkIdentical(stuff$A, rep(1:2, c(ncol(se), ncol(se2))))
checkIdentical(stuff$B, rep(c(NA, 3), c(ncol(se), ncol(se2))))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), 12)))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(2, nrow(se2))))
# Assay data is correctly combined.
mat <- as.matrix(assay(stuff))
ref <- cbind(
rbind(assay(se), matrix(NA, 12, ncol(se))),
rbind(NA, NA, assay(se2))
)
rownames(ref) <- letters[1:22]
checkIdentical(mat, ref)
mat <- as.matrix(assay(stuff, 2))
ref <- cbind(
matrix(NA, nrow(stuff), ncol(se)),
rbind(NA, NA, assay(se2, 2))
)
rownames(ref) <- letters[1:22]
checkIdentical(mat, ref)
# Unary methods work as expected.
checkIdentical(se, combineCols(se, delayed=FALSE))
}
test_combineCols_assays <- function() {
# Deep dive into correct assay name behavior.
se <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10),
matrix(rnorm(1000), ncol=10)))
colnames(se) <- letters[1:10]
colnames(se2) <- letters[15:24]
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# This should fail due to differences in the number of _unnamed_ assays.
checkException(combineCols(se, se2), silent=TRUE)
# Either all assays are named, or all are unnamed.
assays(se) <- assays(se)[c(1, 1)]
assayNames(se2) <- c("WHEE", "BLAH")
checkException(combineCols(se, se2), silent=TRUE)
assays(se2) <- unname(assays(se2))
out <- combineCols(se, se2)
checkIdentical(colnames(out), letters[c(1:10, 15:24)])
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
}
test_combineCols_ranges_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("GENE_", 21:120)
# Checking that an SE is returned.
out <- combineCols(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), rownames(se)) # ignoring other row names when use.names=FALSE.
out <- combineCols(se, se2)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), union(rownames(se), rownames(se2)))
# Checking that an RSE is returned.
ref <- GRanges("chrA", IRanges(1, 1:120), seqinfo=Seqinfo(seqlengths=c(chrA=1000)))
names(ref) <- paste0("GENE_", 1:120)
rowRanges(se) <- ref[1:100]
rowRanges(se2) <- ref[21:120]
suppressWarnings(out <- combineCols(se, se2, use.names=FALSE)) # should have a warning here due to differences in values.
checkIdentical(as.character(class(out)), "RangedSummarizedExperiment")
checkIdentical(rowRanges(out), rowRanges(se))
out <- combineCols(se, se2)
checkIdentical(rowRanges(out), ref)
# Checking that it works with mixtures of object classes in rowRanges.
se3 <- se2
rowRanges(se3) <- NULL
rownames(se3) <- rownames(se2)
out <- combineCols(se, se3)
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(rownames(out), paste0("GENE_", 1:120))
checkIdentical(unname(lengths(rowRanges(out))), rep(1:0, c(100, 20)))
out2 <- combineCols(se3, se) # flipping the order.
checkIdentical(rownames(out2), paste0("GENE_", c(21:120, 1:20)))
checkIdentical(unname(lengths(rowRanges(out2))), rep(c(1L,0L,1L), c(80, 20, 20)))
out3 <- combineCols(se, se2, se3)
checkIdentical(rowRanges(out3), ref) # avoid unnecessary conversion to a GRL.
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
out <- combineCols(se, se4)
checkIdentical(rowRanges(out), as(ref, "GRangesList"))
# Checking that we get the same object class, regardless of ordering of inputs.
checkIdentical(rowRanges(out), rowRanges(combineCols(se, se3, se4)))
checkIdentical(rowRanges(out), rowRanges(combineCols(se3, se, se4))[rownames(out)])
checkIdentical(rowRanges(out), rowRanges(combineCols(se3, se4, se))[rownames(out)])
# Handles conflicting features correctly.
se5 <- se2
strand(rowRanges(se5)[1]) <- "+"
suppressWarnings(out <- combineCols(se, se5)) # this should emit a warning.
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(1:0, c(100, 20)))
}
test_combineCols_ranges_unnamed <- function() {
# Repeating the same suite of tests for SEs without rownames.
# This checks the correctness of some edge-case behaviors.
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
# Checking that an SE is returned.
out <- combineCols(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(nrow(out), nrow(se))
checkException(combineCols(se, se2), silent=TRUE)
# Checking that an RSE is returned.
ref <- GRanges("chrA", IRanges(1, 1:120), seqinfo=Seqinfo(seqlengths=c(chrA=1000)))
rowRanges(se) <- ref[1:100]
rowRanges(se2) <- ref[21:120]
suppressWarnings(out <- combineCols(se, se2, use.names=FALSE)) # should have a warning here due to differences in values.
checkIdentical(as.character(class(out)), "RangedSummarizedExperiment")
checkIdentical(rowRanges(out), rowRanges(se))
# Checking that mixtures of objects work.
se3 <- se2
rowRanges(se3) <- NULL
out <- combineCols(se, se3, use.names=FALSE) # no warning.
checkIdentical(rowRanges(out), rowRanges(se))
out2 <- combineCols(se3, se, use.names=FALSE)
checkIdentical(rowRanges(out2), rowRanges(se))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineCols(se, se4, use.names=FALSE)) # has warning.
checkIdentical(rowRanges(out), as(rowRanges(se), "GRangesList"))
se5 <- se
rowRanges(se5) <- as(rowRanges(se5), "GRangesList")
out <- combineCols(se, se5, use.names=FALSE) # no warning.
checkIdentical(rowRanges(out), as(rowRanges(se), "GRangesList"))
multi.com <- suppressWarnings(combineCols(se, se3, se4, use.names=FALSE))
checkIdentical(rowRanges(out), rowRanges(multi.com))
}
Bioconductor/SummarizedExperiment documentation built on Nov. 2, 2024, 8:20 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
test_combineRows_unnamed <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10),
normalized=matrix(rnorm(1000), ncol=10)))
colData(se2)$B <- 2
rowData(se2)$B <- "B"
stuff <- combineRows(se, se2, use.names=FALSE)
# Column data is correctly combined.
checkIdentical(stuff$A, rep(1, ncol(stuff)))
checkIdentical(stuff$B, rep(2, ncol(stuff)))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), nrow(se2))))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(nrow(se), nrow(se2))))
# Assay data is correctly combined.
checkIdentical(as.matrix(assay(stuff)), rbind(assay(se), assay(se2)))
checkIdentical(as.matrix(assay(stuff, 2)), rbind(matrix(NA, nrow(se), ncol(se)), assay(se2, 2)))
# Unary methods work as expected.
checkIdentical(se, combineRows(se, delayed=FALSE, use.names=FALSE))
}
test_combineRows_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=20),
normalized=matrix(rnorm(1000), ncol=20)))
colData(se2)$B <- 2
rowData(se2)$B <- "B"
# This fails, because we expect matching numbers of columns when use.names=TRUE.
checkException(combineRows(se, se2), silent=TRUE)
colnames(se) <- letters[1:10]
colnames(se2) <- letters[3:22]
stuff <- combineRows(se, se2)
# Column data is correctly combined
checkIdentical(colnames(stuff), letters[1:22])
checkIdentical(stuff$A, rep(c(1, NA), c(ncol(se), 12)))
checkIdentical(stuff$B, rep(c(NA, 2), c(2, ncol(se2))))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), nrow(se2))))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(nrow(se), nrow(se2))))
# Assay data is correctly combined.
mat <- as.matrix(assay(stuff))
ref <- rbind(
cbind(assay(se), matrix(NA, nrow(se), ncol=12)),
cbind(NA, NA, assay(se2))
)
colnames(ref) <- letters[1:22]
checkIdentical(mat, ref)
mat <- as.matrix(assay(stuff, 2))
ref <- rbind(
matrix(NA, nrow(se), ncol(stuff)),
cbind(NA, NA, assay(se2, 2))
)
colnames(ref) <- letters[1:22]
checkIdentical(mat, ref)
# Unary methods work as expected.
checkIdentical(se, combineRows(se, delayed=FALSE))
}
test_combineRows_assays <- function() {
# Deep dive into correct assay name behavior.
se <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10),
matrix(rnorm(1000), ncol=10)))
colnames(se) <- letters[1:10]
colnames(se2) <- letters[15:24]
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# This should fail due to differences in the number of _unnamed_ assays.
checkException(combineRows(se, se2), silent=TRUE)
# Either all assays are named, or all are unnamed.
assays(se) <- assays(se)[c(1, 1)]
assayNames(se2) <- c("WHEE", "BLAH")
checkException(combineRows(se, se2), silent=TRUE)
assays(se2) <- unname(assays(se2))
out <- combineRows(se, se2)
checkIdentical(colnames(out), letters[c(1:10, 15:24)])
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
}
test_combineRows_ranges_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# Returns a vanilla SE.
out <- combineRows(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
# Returns a GRanges.
replace <- GRanges("chrA", IRanges(1, 1:100))
names(replace) <- rownames(se)
rowRanges(se) <- replace
replace2 <- GRanges("chrB", IRanges(1, 1:100))
names(replace2) <- rownames(se2)
rowRanges(se2) <- replace2
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rowRanges(out), suppressWarnings(c(replace, replace2)))
# Testing different objects.
se3 <- se2
rowRanges(se3) <- NULL
rownames(se3) <- rownames(se2)
suppressWarnings(out <- combineRows(se, se3, use.names=FALSE))
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(c(1L, 0L), c(nrow(se), nrow(se3))))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineRows(se, se4, use.names=FALSE))
expected <- suppressWarnings(as(c(replace, replace2), "GRangesList"))
checkIdentical(rowRanges(out), expected)
# Order doesn't affect conversion to GRL.
suppressWarnings(out <- combineRows(se4, se, use.names=FALSE))
expected <- suppressWarnings(as(c(replace2, replace), "GRangesList"))
checkIdentical(rowRanges(out), expected)
suppressWarnings(combined <- rowRanges(combineRows(se, se3, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(1L, 0L, 1L), c(nrow(se), nrow(se3), nrow(se4))))
suppressWarnings(combined <- rowRanges(combineRows(se3, se, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(0L, 1L, 1L), c(nrow(se3), nrow(se), nrow(se4))))
}
test_combineRows_ranges_unnamed <- function() {
# Repeating the same suite of tests for SEs without rownames.
# This checks the correctness of some edge-case behaviors.
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
# Returns a vanilla SE.
out <- combineRows(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(nrow(out), nrow(se) + nrow(se2))
# Returns a GRanges.
rowRanges(se) <- GRanges("chrA", IRanges(1, 1:100))
rowRanges(se2) <- GRanges("chrB", IRanges(1, 1:100))
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rowRanges(out), suppressWarnings(c(rowRanges(se), rowRanges(se2))))
# Testing different objects.
se3 <- se2
rowRanges(se3) <- NULL
suppressWarnings(out <- combineRows(se, se3, use.names=FALSE))
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(c(1L, 0L), c(nrow(se), nrow(se3))))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineRows(se, se4, use.names=FALSE))
expected <- suppressWarnings(as(c(rowRanges(se), rowRanges(se2)), "GRangesList"))
checkIdentical(rowRanges(out), expected)
suppressWarnings(combined <- rowRanges(combineRows(se, se3, se4, use.names=FALSE)))
checkIdentical(unname(lengths(combined)), rep(c(1L, 0L, 1L), c(nrow(se), nrow(se3), nrow(se4))))
# Handles partial row names.
rownames(se) <- paste0("GENE_", 1:100)
suppressWarnings(out <- combineRows(se, se2, use.names=FALSE))
checkIdentical(rownames(out), c(rownames(se), character(nrow(se2))))
}
test_combineCols_unnamed <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
colData(se)$A <- 1L
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10),
normalized=matrix(rnorm(1000), ncol=10)))
colData(se2)$A <- 2L
colData(se2)$B <- 3
rowData(se2)$B <- "B"
stuff <- combineCols(se, se2, use.names=FALSE)
# Column data is correctly combined.
checkIdentical(stuff$A, rep(1:2, each=10))
checkIdentical(stuff$B, rep(c(NA, 3), each=10))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(1, nrow(se)))
checkIdentical(rowData(stuff)$B, rep("B", nrow(se)))
# Assay data is correctly combined.
checkIdentical(as.matrix(assay(stuff)), cbind(assay(se), assay(se2)))
checkIdentical(as.matrix(assay(stuff, 2)), cbind(matrix(NA, nrow(se), ncol(se)), assay(se2, 2)))
# Unary methods work as expected.
checkIdentical(se, combineCols(se, delayed=FALSE, use.names=FALSE))
}
test_combineCols_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=100)))
colData(se)$A <- 1L
rowData(se)$A <- 1
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=50),
normalized=matrix(rnorm(1000), ncol=50)))
colData(se2)$A <- 2L
colData(se2)$B <- 3
rowData(se2)$B <- "B"
# This fails, because we expect matching numbers of columns when use.names=TRUE.
checkException(combineCols(se, se2), silent=TRUE)
rownames(se) <- letters[1:10]
rownames(se2) <- letters[3:22]
stuff <- combineCols(se, se2)
# Column data is correctly combined
checkIdentical(rownames(stuff), letters[1:22])
checkIdentical(stuff$A, rep(1:2, c(ncol(se), ncol(se2))))
checkIdentical(stuff$B, rep(c(NA, 3), c(ncol(se), ncol(se2))))
# Row data is correctly combined.
checkIdentical(rowData(stuff)$A, rep(c(1, NA), c(nrow(se), 12)))
checkIdentical(rowData(stuff)$B, rep(c(NA, "B"), c(2, nrow(se2))))
# Assay data is correctly combined.
mat <- as.matrix(assay(stuff))
ref <- cbind(
rbind(assay(se), matrix(NA, 12, ncol(se))),
rbind(NA, NA, assay(se2))
)
rownames(ref) <- letters[1:22]
checkIdentical(mat, ref)
mat <- as.matrix(assay(stuff, 2))
ref <- cbind(
matrix(NA, nrow(stuff), ncol(se)),
rbind(NA, NA, assay(se2, 2))
)
rownames(ref) <- letters[1:22]
checkIdentical(mat, ref)
# Unary methods work as expected.
checkIdentical(se, combineCols(se, delayed=FALSE))
}
test_combineCols_assays <- function() {
# Deep dive into correct assay name behavior.
se <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(matrix(rpois(1000, 10), ncol=10),
matrix(rnorm(1000), ncol=10)))
colnames(se) <- letters[1:10]
colnames(se2) <- letters[15:24]
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("SPIKE_", 1:100)
# This should fail due to differences in the number of _unnamed_ assays.
checkException(combineCols(se, se2), silent=TRUE)
# Either all assays are named, or all are unnamed.
assays(se) <- assays(se)[c(1, 1)]
assayNames(se2) <- c("WHEE", "BLAH")
checkException(combineCols(se, se2), silent=TRUE)
assays(se2) <- unname(assays(se2))
out <- combineCols(se, se2)
checkIdentical(colnames(out), letters[c(1:10, 15:24)])
checkIdentical(rownames(out), c(rownames(se), rownames(se2)))
}
test_combineCols_ranges_named <- function() {
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
rownames(se) <- paste0("GENE_", 1:100)
rownames(se2) <- paste0("GENE_", 21:120)
# Checking that an SE is returned.
out <- combineCols(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), rownames(se)) # ignoring other row names when use.names=FALSE.
out <- combineCols(se, se2)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(rownames(out), union(rownames(se), rownames(se2)))
# Checking that an RSE is returned.
ref <- GRanges("chrA", IRanges(1, 1:120), seqinfo=Seqinfo(seqlengths=c(chrA=1000)))
names(ref) <- paste0("GENE_", 1:120)
rowRanges(se) <- ref[1:100]
rowRanges(se2) <- ref[21:120]
suppressWarnings(out <- combineCols(se, se2, use.names=FALSE)) # should have a warning here due to differences in values.
checkIdentical(as.character(class(out)), "RangedSummarizedExperiment")
checkIdentical(rowRanges(out), rowRanges(se))
out <- combineCols(se, se2)
checkIdentical(rowRanges(out), ref)
# Checking that it works with mixtures of object classes in rowRanges.
se3 <- se2
rowRanges(se3) <- NULL
rownames(se3) <- rownames(se2)
out <- combineCols(se, se3)
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(rownames(out), paste0("GENE_", 1:120))
checkIdentical(unname(lengths(rowRanges(out))), rep(1:0, c(100, 20)))
out2 <- combineCols(se3, se) # flipping the order.
checkIdentical(rownames(out2), paste0("GENE_", c(21:120, 1:20)))
checkIdentical(unname(lengths(rowRanges(out2))), rep(c(1L,0L,1L), c(80, 20, 20)))
out3 <- combineCols(se, se2, se3)
checkIdentical(rowRanges(out3), ref) # avoid unnecessary conversion to a GRL.
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
out <- combineCols(se, se4)
checkIdentical(rowRanges(out), as(ref, "GRangesList"))
# Checking that we get the same object class, regardless of ordering of inputs.
checkIdentical(rowRanges(out), rowRanges(combineCols(se, se3, se4)))
checkIdentical(rowRanges(out), rowRanges(combineCols(se3, se, se4))[rownames(out)])
checkIdentical(rowRanges(out), rowRanges(combineCols(se3, se4, se))[rownames(out)])
# Handles conflicting features correctly.
se5 <- se2
strand(rowRanges(se5)[1]) <- "+"
suppressWarnings(out <- combineCols(se, se5)) # this should emit a warning.
checkTrue(is(rowRanges(out), "GRangesList"))
checkIdentical(unname(lengths(rowRanges(out))), rep(1:0, c(100, 20)))
}
test_combineCols_ranges_unnamed <- function() {
# Repeating the same suite of tests for SEs without rownames.
# This checks the correctness of some edge-case behaviors.
se <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
se2 <- SummarizedExperiment(list(counts=matrix(rpois(1000, 10), ncol=10)))
# Checking that an SE is returned.
out <- combineCols(se, se2, use.names=FALSE)
checkIdentical(as.character(class(out)), "SummarizedExperiment")
checkIdentical(nrow(out), nrow(se))
checkException(combineCols(se, se2), silent=TRUE)
# Checking that an RSE is returned.
ref <- GRanges("chrA", IRanges(1, 1:120), seqinfo=Seqinfo(seqlengths=c(chrA=1000)))
rowRanges(se) <- ref[1:100]
rowRanges(se2) <- ref[21:120]
suppressWarnings(out <- combineCols(se, se2, use.names=FALSE)) # should have a warning here due to differences in values.
checkIdentical(as.character(class(out)), "RangedSummarizedExperiment")
checkIdentical(rowRanges(out), rowRanges(se))
# Checking that mixtures of objects work.
se3 <- se2
rowRanges(se3) <- NULL
out <- combineCols(se, se3, use.names=FALSE) # no warning.
checkIdentical(rowRanges(out), rowRanges(se))
out2 <- combineCols(se3, se, use.names=FALSE)
checkIdentical(rowRanges(out2), rowRanges(se))
se4 <- se2
rowRanges(se4) <- as(rowRanges(se4), "GRangesList")
suppressWarnings(out <- combineCols(se, se4, use.names=FALSE)) # has warning.
checkIdentical(rowRanges(out), as(rowRanges(se), "GRangesList"))
se5 <- se
rowRanges(se5) <- as(rowRanges(se5), "GRangesList")
out <- combineCols(se, se5, use.names=FALSE) # no warning.
checkIdentical(rowRanges(out), as(rowRanges(se), "GRangesList"))
multi.com <- suppressWarnings(combineCols(se, se3, se4, use.names=FALSE))
checkIdentical(rowRanges(out), rowRanges(multi.com))
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.