tests/testthat/test-FitAndFitMS.R
In Nik-Zainal-Group/signature.tools.lib: signature.tools.lib
context("testing functions Fit and FitMS")
test_that("test that Fit() works on a random matrix, using useBootstrap=FALSE", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
threshold_percent = 0.1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
threshold_p.value = 0.1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix with useBootstrap=TRUE, and that random seed works, no parallel", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 5
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res1 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 1,
randomSeed = 1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 1,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that Fit() works on a random matrix with useBootstrap=TRUE, and that random seed works, using parallel", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 5
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res1 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 2,
randomSeed = 1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 2,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that plotFit() works on a random matrix", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
threshold_p.value = 0.1)
plotFit(res,outdir = "test_fit/")
unlink("test_fit/", recursive = TRUE)
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with multiStepMode=constrainedFit works with useBootstrap=FALSE then plots", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
threshold_percent = 0.1)
plotFitMS(res,outdir = "test_fit/")
unlink("test_fit/", recursive = TRUE)
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with multiStepMode=constrainedFit with useBootstrap=TRUE and randomSeed, no parallal", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res1 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 1,
randomSeed = 1)
res2 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 1,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that FitMS() with multiStepMode=constrainedFit with useBootstrap=TRUE and randomSeed, use parallal", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res1 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 2,
randomSeed = 1)
res2 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 2,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that FitMS() with different common and rare signatures tiers", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T2",
rareSignatureTier = "T0")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T3",
rareSignatureTier = "T1")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T1",
rareSignatureTier = "T3")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T2",
rareSignatureTier = "T4")
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with different rare signatures selection criteria", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
rareCandidateSelectionCriteria = "MinError")
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with Gini-based threshold", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
exposureFilterType = "giniScaledThreshold")
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=FALSE, deactivate thresholds", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
threshold_percent = -1,
threshold_nmuts = -1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = -1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE, deactivate thresholds", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = -1,
threshold_nmuts = -1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = -1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE, nmuts thresholds only", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = -1,
threshold_nmuts = 10)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = 10)
#here goes the test
expect_true(TRUE)
})
Nik-Zainal-Group/signature.tools.lib documentation built on April 13, 2025, 5:50 p.m.
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context("testing functions Fit and FitMS")
test_that("test that Fit() works on a random matrix, using useBootstrap=FALSE", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
threshold_percent = 0.1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
threshold_p.value = 0.1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix with useBootstrap=TRUE, and that random seed works, no parallel", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 5
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res1 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 1,
randomSeed = 1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 1,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that Fit() works on a random matrix with useBootstrap=TRUE, and that random seed works, using parallel", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 5
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res1 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 2,
randomSeed = 1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0,
threshold_p.value = 0.1,
nparallel = 2,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that plotFit() works on a random matrix", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
threshold_p.value = 0.1)
plotFit(res,outdir = "test_fit/")
unlink("test_fit/", recursive = TRUE)
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with multiStepMode=constrainedFit works with useBootstrap=FALSE then plots", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
threshold_percent = 0.1)
plotFitMS(res,outdir = "test_fit/")
unlink("test_fit/", recursive = TRUE)
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with multiStepMode=constrainedFit with useBootstrap=TRUE and randomSeed, no parallal", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res1 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 1,
randomSeed = 1)
res2 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 1,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that FitMS() with multiStepMode=constrainedFit with useBootstrap=TRUE and randomSeed, use parallal", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res1 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 2,
randomSeed = 1)
res2 <- FitMS(catalogues = catalogues,
organ = "Breast",
multiStepMode = "constrainedFit",
useBootstrap = TRUE,
nboot = 5,
threshold_percent = 0.1,
nparallel = 2,
randomSeed = 1)
#here goes the test
expect_equal(res1$exposures,res2$exposures)
})
test_that("test that FitMS() with different common and rare signatures tiers", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T2",
rareSignatureTier = "T0")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T3",
rareSignatureTier = "T1")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T1",
rareSignatureTier = "T3")
res <- FitMS(catalogues = catalogues,
organ = "Breast",
commonSignatureTier = "T2",
rareSignatureTier = "T4")
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with different rare signatures selection criteria", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
rareCandidateSelectionCriteria = "MinError")
#here goes the test
expect_true(TRUE)
})
test_that("test that FitMS() with Gini-based threshold", {
#test substitutions
catalogues <- read.table("FitAndFitMStests/FitandFitMStestCatalogues.tsv",sep = "\t",check.names = F,header = T,stringsAsFactors = F)
res <- FitMS(catalogues = catalogues,
organ = "Breast",
exposureFilterType = "giniScaledThreshold")
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=FALSE, deactivate thresholds", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
threshold_percent = -1,
threshold_nmuts = -1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = FALSE,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = -1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE, deactivate thresholds", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = -1,
threshold_nmuts = -1)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = -1)
#here goes the test
expect_true(TRUE)
})
test_that("test that Fit() works on a random matrix, using useBootstrap=TRUE, nmuts thresholds only", {
#test substitutions
mut.order <- c("A[C>A]A","A[C>A]C","A[C>A]G","A[C>A]T","C[C>A]A","C[C>A]C","C[C>A]G","C[C>A]T","G[C>A]A","G[C>A]C","G[C>A]G","G[C>A]T","T[C>A]A","T[C>A]C","T[C>A]G","T[C>A]T","A[C>G]A","A[C>G]C","A[C>G]G","A[C>G]T","C[C>G]A","C[C>G]C","C[C>G]G","C[C>G]T","G[C>G]A","G[C>G]C","G[C>G]G","G[C>G]T","T[C>G]A","T[C>G]C","T[C>G]G","T[C>G]T","A[C>T]A","A[C>T]C","A[C>T]G","A[C>T]T","C[C>T]A","C[C>T]C","C[C>T]G","C[C>T]T","G[C>T]A","G[C>T]C","G[C>T]G","G[C>T]T","T[C>T]A","T[C>T]C","T[C>T]G","T[C>T]T","A[T>A]A","A[T>A]C","A[T>A]G","A[T>A]T","C[T>A]A","C[T>A]C","C[T>A]G","C[T>A]T","G[T>A]A","G[T>A]C","G[T>A]G","G[T>A]T","T[T>A]A","T[T>A]C","T[T>A]G","T[T>A]T","A[T>C]A","A[T>C]C","A[T>C]G","A[T>C]T","C[T>C]A","C[T>C]C","C[T>C]G","C[T>C]T","G[T>C]A","G[T>C]C","G[T>C]G","G[T>C]T","T[T>C]A","T[T>C]C","T[T>C]G","T[T>C]T","A[T>G]A","A[T>G]C","A[T>G]G","A[T>G]T","C[T>G]A","C[T>G]C","C[T>G]G","C[T>G]T","G[T>G]A","G[T>G]C","G[T>G]G","G[T>G]T","T[T>G]A","T[T>G]C","T[T>G]G","T[T>G]T")
n_row <- 96
n_col <- 15
rnd_matrix <- round(matrix(runif(n_row*n_col,min = 0,max = 50),nrow = n_row,ncol = n_col))
colnames(rnd_matrix) <- paste0("C",1:n_col)
row.names(rnd_matrix) <- mut.order
res <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
threshold_percent = -1,
threshold_nmuts = 10)
res2 <- Fit(catalogues = rnd_matrix,
signatures = cosmic30,
useBootstrap = TRUE,
nboot = 5,
exposureFilterType = "giniScaledThreshold",
giniThresholdScaling = -1,
giniThresholdScaling_nmuts = 10)
#here goes the test
expect_true(TRUE)
})
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