Nothing
tests/testthat/test.samplePop.R
In OncoSimulR: Forward Genetic Simulation of Cancer Progression with Epistasis
inittime <- Sys.time()
cat(paste("\n Starting samplePop tests", date(), "\n"))
## RNGkind("Mersenne-Twister")
test_that("exercising the sampling code, v1 objects", {
data(examplePosets)
p705 <- examplePosets[["p705"]]
r1 <- oncoSimulIndiv(p705,
sampleEvery = 0.03, keepEvery = 1
)
p1 <- oncoSimulPop(4, p705, numPassengers = 30, mc.cores = 2,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1 ),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "whole", timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "single", timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole", timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "single", timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "whole", timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "single", timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
})
test_that("exercising the sampling code, v1 objects, possibly NAs", {
data(examplePosets)
p705 <- examplePosets[["p705"]]
r1 <- oncoSimulIndiv(p705, numPassengers = 30,
sampleEvery = 0.03, keepEvery = 1,
onlyCancer = FALSE)
p1 <- oncoSimulPop(4, p705, mc.cores = 2, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(r1),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
})
test_that("exercising the sampling code, v1 objects, possibly NAs, more", {
data(examplePosets)
p1101 <- examplePosets[["p1101"]]
r1 <- oncoSimulIndiv(p1101, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
p1 <- oncoSimulPop(4, p1101, mc.cores = 2, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(r1),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
})
test_that("exercising the sampling code, v2 objects, possibly NAs in output", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2") )
o1 <- oncoSimulIndiv(oi, detectionSize = 1e4,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(2,
oi,
detectionSize = 1e4,
mc.cores = 2,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
## many of them are generating warnings, because sampling
## with pop size of 0. That is OK.
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
})
test_that("exercising the sampling code, v2 objects, possibly NAs in output, more", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = FALSE,
mc.cores = 2,
sampleEvery = 0.03, keepEvery = 1)
## many of them are generating warnings, because sampling
## with pop size of 0. That is OK.
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising the sampling code, v2 objects", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2") )
o1 <- oncoSimulIndiv(oi, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(2,
oi,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
})
test_that("exercising the sampling code, v2 objects, more", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising sampling code, single sampled period", {
o3init <- allFitnessEffects(orderEffects = c(
"M > D > F" = 0.99,
"D > M > F" = 0.2,
"D > M" = 0.1,
"M > D" = 0.9),
noIntGenes = c("u" = 0.01,
"v" = 0.01,
"w" = 0.001,
"x" = 0.0001,
"y" = -0.0001,
"z" = 0.001),
geneToModule =
c("Root" = "Root",
"M" = "m",
"F" = "f",
"D" = "d") )
for(i in 1:10) {
i1 <- oncoSimulIndiv(o3init, model = "Exp", initSize = 1e8,
mu = 1e-3, finalTime = .01,
detectionDrivers = 2,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1
)
expect_message(spi <- samplePop(i1, timeSample = "unif"),
"Subjects", fixed = TRUE)
}
})
test_that("exercising sampling code, customSize", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1, popSizeSample = 2100),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_warning(samplePop(o1, popSizeSample = 21000),
"Pop size never", fixed = TRUE)
expect_message(samplePop(o4, popSizeSample = c(6100)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, popSizeSample = c(6100, 6000, 8999, 8030)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, popSizeSample = c(6100, 6000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
## this was fixed to not give warnings
## expect_warning(samplePop(o4, popSizeSample = c(6100, 6000)),
## "length popSizeSample != number of subjects")
expect_warning(samplePop(o4, popSizeSample = 21000),
"Pop size never >= requested size", fixed = TRUE)
expect_message(samplePop(o4, typeSample = "single",
popSizeSample = c(6100, 0, 5000, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
popSizeSample = c(9000, 9000, 8500, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
## these are specific for the nowt code to exercise the dealing with
## borderline cases and the second to deal with a clearly non-borderline
o41 <- oncoSimulPop(4,
cbn1,
initSize = 2e3,
detectionSize = 1e3,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o41, typeSample = "single-nowt",
popSizeSample = c(900, 800, 850, 900)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_warning(samplePop(o41, typeSample = "single-nowt",
popSizeSample = c(900, 800, 850, 900)),
"No non-WT clone with required popSize or at required time")
o91 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e5,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o91, typeSample = "single-nowt",
popSizeSample = c(9000, 9000, 8500, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising sampling code, customSize", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs, drvNames = c("a", "b", "c", "d", "e", "g"))
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e8,
onlyCancer = TRUE,
detectionDrivers = 1,
max.num.tries = 5000,
sampleEvery = 0.03,
keepEvery = 1000000)
expect_message(samplePop(o1, timeSample = "unif"),
"Only one sampled time period with mutants", fixed = TRUE)
})
test_that("Exercise sampledGenotypes, option for selecting genes", {
initS <- 200
u <- 0.2; i <- -0.02; vi <- 0.6; ui <- uv <- -Inf
od <- allFitnessEffects(
epistasis = c("u" = u, "u:i" = ui,
"u:v" = uv, "i" = i,
"v:-i" = -Inf, "v:i" = vi))
## drvNames = c("u", "v"))
odm <- allMutatorEffects(noIntGenes = c("i" = 50))
evalAllGenotypesFitAndMut(od, odm, addwt = TRUE)
op <- oncoSimulPop(20, od, muEF = odm, model = "McFL",
mu = 1e-4,
onlyCancer = TRUE, finalTime = 15000, detectionSize = NA, detectionProb = NA,
initSize = initS,
keepEvery = NA,
fixation = c("u", "v"),
mc.cores = 2
)
sp <- samplePop(op)
expect_output(print(sampledGenotypes(sp, genes = c("u", "i"))))
expect_output(print(summary(sampledGenotypes(sp, genes = c("u", "i")))))
expect_output(print(sampledGenotypes(sp)))
expect_output(print(summary(sampledGenotypes(sp))))
})
test_that("exercising sampling code, propError", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_error(samplePop(o4, propError = 1.4),
"Proportion with error cannot be > 1", fixed = TRUE)
expect_message(samplePop(o4, propError = 0),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.1),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.2),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.3),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.9),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.01),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.05),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 1),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
})
test_that("sampledGenotypes deals with NAs", {
sp <- structure(c(1, NA, 1, 0, 0, NA, 0, 0, 0, NA, 0, 0, 0, NA, 0,
0, 0, NA, 1, 0, 0, NA, 0, 0, 0, NA, 0, 0, 1, NA, 1, 0),
.Dim = c(4L,
8L),
.Dimnames = list(NULL, c("ZZZ", "APC", "EVC2",
"VVV",
"KRAS", "PIK3CA", "TCF7L2", "TP53")))
sg <- sampledGenotypes(sp)
expect_true(is.na(sg[4, 1]))
expect_true(sg[1, 1] == "WT")
})
cat(paste("\n Ending samplePop tests", date(), "\n"))
cat(paste(" Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
rm(inittime)
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inittime <- Sys.time()
cat(paste("\n Starting samplePop tests", date(), "\n"))
## RNGkind("Mersenne-Twister")
test_that("exercising the sampling code, v1 objects", {
data(examplePosets)
p705 <- examplePosets[["p705"]]
r1 <- oncoSimulIndiv(p705,
sampleEvery = 0.03, keepEvery = 1
)
p1 <- oncoSimulPop(4, p705, numPassengers = 30, mc.cores = 2,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1 ),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "whole", timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(p1, typeSample = "single", timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole", timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "single", timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "whole", timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
expect_message(samplePop(r1, typeSample = "single", timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 7 genes")
})
test_that("exercising the sampling code, v1 objects, possibly NAs", {
data(examplePosets)
p705 <- examplePosets[["p705"]]
r1 <- oncoSimulIndiv(p705, numPassengers = 30,
sampleEvery = 0.03, keepEvery = 1,
onlyCancer = FALSE)
p1 <- oncoSimulPop(4, p705, mc.cores = 2, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 7 genes")
expect_message(samplePop(r1),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 37 genes")
})
test_that("exercising the sampling code, v1 objects, possibly NAs, more", {
data(examplePosets)
p1101 <- examplePosets[["p1101"]]
r1 <- oncoSimulIndiv(p1101, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
p1 <- oncoSimulPop(4, p1101, mc.cores = 2, onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(p1),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(p1, typeSample = "single"),
"Subjects by Genes matrix of 4 subjects and 11 genes")
expect_message(samplePop(r1),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
expect_message(samplePop(r1, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 1 subjects and 11 genes")
})
test_that("exercising the sampling code, v2 objects, possibly NAs in output", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2") )
o1 <- oncoSimulIndiv(oi, detectionSize = 1e4,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(2,
oi,
detectionSize = 1e4,
mc.cores = 2,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
## many of them are generating warnings, because sampling
## with pop size of 0. That is OK.
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
})
test_that("exercising the sampling code, v2 objects, possibly NAs in output, more", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = FALSE,
mc.cores = 2,
sampleEvery = 0.03, keepEvery = 1)
## many of them are generating warnings, because sampling
## with pop size of 0. That is OK.
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising the sampling code, v2 objects", {
oi <- allFitnessEffects(orderEffects =
c("F > D" = -0.3, "D > F" = 0.4),
noIntGenes = rexp(5, 10),
geneToModule =
c("Root" = "Root",
"F" = "f1, f2, f3",
"D" = "d1, d2") )
o1 <- oncoSimulIndiv(oi, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(2,
oi,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 10 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "last"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "uniform"),
"Subjects by Genes matrix of 2 subjects and 10 genes")
})
test_that("exercising the sampling code, v2 objects, more", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "single",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "unif"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o1, typeSample = "whole",
timeSample = "last"),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_message(samplePop(o4),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "unif",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, timeSample = "last",
typeSample = "whole"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "last"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
timeSample = "uniform"),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising sampling code, single sampled period", {
o3init <- allFitnessEffects(orderEffects = c(
"M > D > F" = 0.99,
"D > M > F" = 0.2,
"D > M" = 0.1,
"M > D" = 0.9),
noIntGenes = c("u" = 0.01,
"v" = 0.01,
"w" = 0.001,
"x" = 0.0001,
"y" = -0.0001,
"z" = 0.001),
geneToModule =
c("Root" = "Root",
"M" = "m",
"F" = "f",
"D" = "d") )
for(i in 1:10) {
i1 <- oncoSimulIndiv(o3init, model = "Exp", initSize = 1e8,
mu = 1e-3, finalTime = .01,
detectionDrivers = 2,
onlyCancer = FALSE,
sampleEvery = 0.03, keepEvery = 1
)
expect_message(spi <- samplePop(i1, timeSample = "unif"),
"Subjects", fixed = TRUE)
}
})
test_that("exercising sampling code, customSize", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e4,
onlyCancer = TRUE,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o1, popSizeSample = 2100),
"Subjects by Genes matrix of 1 subjects and 6 genes")
expect_warning(samplePop(o1, popSizeSample = 21000),
"Pop size never", fixed = TRUE)
expect_message(samplePop(o4, popSizeSample = c(6100)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, popSizeSample = c(6100, 6000, 8999, 8030)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, popSizeSample = c(6100, 6000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
## this was fixed to not give warnings
## expect_warning(samplePop(o4, popSizeSample = c(6100, 6000)),
## "length popSizeSample != number of subjects")
expect_warning(samplePop(o4, popSizeSample = 21000),
"Pop size never >= requested size", fixed = TRUE)
expect_message(samplePop(o4, typeSample = "single",
popSizeSample = c(6100, 0, 5000, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_message(samplePop(o4, typeSample = "single-nowt",
popSizeSample = c(9000, 9000, 8500, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
## these are specific for the nowt code to exercise the dealing with
## borderline cases and the second to deal with a clearly non-borderline
o41 <- oncoSimulPop(4,
cbn1,
initSize = 2e3,
detectionSize = 1e3,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o41, typeSample = "single-nowt",
popSizeSample = c(900, 800, 850, 900)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
expect_warning(samplePop(o41, typeSample = "single-nowt",
popSizeSample = c(900, 800, 850, 900)),
"No non-WT clone with required popSize or at required time")
o91 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e5,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_message(samplePop(o91, typeSample = "single-nowt",
popSizeSample = c(9000, 9000, 8500, 9000)),
"Subjects by Genes matrix of 4 subjects and 6 genes")
})
test_that("exercising sampling code, customSize", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs, drvNames = c("a", "b", "c", "d", "e", "g"))
o1 <- oncoSimulIndiv(cbn1, detectionSize = 1e8,
onlyCancer = TRUE,
detectionDrivers = 1,
max.num.tries = 5000,
sampleEvery = 0.03,
keepEvery = 1000000)
expect_message(samplePop(o1, timeSample = "unif"),
"Only one sampled time period with mutants", fixed = TRUE)
})
test_that("Exercise sampledGenotypes, option for selecting genes", {
initS <- 200
u <- 0.2; i <- -0.02; vi <- 0.6; ui <- uv <- -Inf
od <- allFitnessEffects(
epistasis = c("u" = u, "u:i" = ui,
"u:v" = uv, "i" = i,
"v:-i" = -Inf, "v:i" = vi))
## drvNames = c("u", "v"))
odm <- allMutatorEffects(noIntGenes = c("i" = 50))
evalAllGenotypesFitAndMut(od, odm, addwt = TRUE)
op <- oncoSimulPop(20, od, muEF = odm, model = "McFL",
mu = 1e-4,
onlyCancer = TRUE, finalTime = 15000, detectionSize = NA, detectionProb = NA,
initSize = initS,
keepEvery = NA,
fixation = c("u", "v"),
mc.cores = 2
)
sp <- samplePop(op)
expect_output(print(sampledGenotypes(sp, genes = c("u", "i"))))
expect_output(print(summary(sampledGenotypes(sp, genes = c("u", "i")))))
expect_output(print(sampledGenotypes(sp)))
expect_output(print(summary(sampledGenotypes(sp))))
})
test_that("exercising sampling code, propError", {
cs <- data.frame(parent = c(rep("Root", 4), "a", "b", "d", "e", "c"),
child = c("a", "b", "d", "e", "c", "c", rep("g", 3)),
s = 0.1,
sh = -0.9,
typeDep = "MN")
cbn1 <- allFitnessEffects(cs)
o4 <- oncoSimulPop(4,
cbn1,
detectionSize = 1e4,
onlyCancer = TRUE,
mc.cores = 2,
max.num.tries = 5000,
sampleEvery = 0.03, keepEvery = 1)
expect_error(samplePop(o4, propError = 1.4),
"Proportion with error cannot be > 1", fixed = TRUE)
expect_message(samplePop(o4, propError = 0),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.1),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.2),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.3),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.9),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.01),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 0.05),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
expect_message(samplePop(o4, propError = 1),
"Subjects by Genes matrix of 4 subjects",
fixed = TRUE)
})
test_that("sampledGenotypes deals with NAs", {
sp <- structure(c(1, NA, 1, 0, 0, NA, 0, 0, 0, NA, 0, 0, 0, NA, 0,
0, 0, NA, 1, 0, 0, NA, 0, 0, 0, NA, 0, 0, 1, NA, 1, 0),
.Dim = c(4L,
8L),
.Dimnames = list(NULL, c("ZZZ", "APC", "EVC2",
"VVV",
"KRAS", "PIK3CA", "TCF7L2", "TP53")))
sg <- sampledGenotypes(sp)
expect_true(is.na(sg[4, 1]))
expect_true(sg[1, 1] == "WT")
})
cat(paste("\n Ending samplePop tests", date(), "\n"))
cat(paste(" Took ", round(difftime(Sys.time(), inittime, units = "secs"), 2), "\n\n"))
rm(inittime)
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