tests/testthat/test_hg38.R
In acc-bioinfo/TMBleR: Tumor Mutational Burden Quantification From Gene Panels And WES
context("applyFilters_hg38.R")
################################################################################
# Helper function
################################################################################
test_missing <- function(x)
{
" Check the number of variants (filtered + passed) is equal to those evaluated by the filter (input vcf) "
if(isFALSE(debug_env$debug)){
print("Set debug_env$debug = TRUE in '/R/globalVariable.R'")
debug_env$debug = TRUE
}
passed.var <- x[[1]][[1]] %>% nrow
filtered.var <- debug_env$filters %>% nrow
input.var <- hg38.vcfs[[1]]@fixed %>% nrow
list(cat("Filtered:", filtered.var
,"\nPassed:", passed.var
,"\nInput Variants:", input.var
,"\nmissing:", input.var - sum(filtered.var, passed.var)))
expect_true( input.var == sum(filtered.var, passed.var) )
}
# Conditions:
# 1. Set debug_env$debug = TRUE
# 2. Launch only after the corresponding filter
#test_missing(hg38.vcfs_nonfiltered)
#test_missing(hg38.vcfs_NoCancer)
# Helper fn to check in the vcf file if the FILTER field contains the expected match
# in the original vcf file used as input. If returns the the FILTER field without the
# expected match
find_expected_filter_type <- function(variant_vector=hg38.vcfs$testhg38@fixed$FILTER, expected_filter_type){
idx_filter <- purrr::map_lgl(variant_vector, ~ {
out <- unlist(strsplit(.x,";", fixed = TRUE))
out <- unlist(strsplit(out, "="))
out <- unlist(strsplit(out, "|", fixed=TRUE))
out <- out == expected_filter_type
return(any(out))
})
return(variant_vector[!idx_filter])
}
################################################################################
# PREPARATION
################################################################################
# Define vcf path and read in vcf files
hg38.vcf_files <- list(testhg38= system.file("extdata", "hg38.test.vcf", package = "TMBleR", mustWork = TRUE))
hg38.vcfs <- readVcfFiles(hg38.vcf_files, assembly = "hg38")
# Read in input the panel sequencing design
designPanel <- readDesign(system.file("extdata"
, "ExamplePanel_design_OnlyChr7ForTest_hg38.bed"
, package = "TMBleR"
, mustWork = TRUE)
, assembly = "hg38")
# ------------------------------------------------------------------------------
# Apply different filters
# ------------------------------------------------------------------------------
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 0: no filters - only filtered due to .bed file & intronic regions
hg38.vcfs_nonfiltered <- applyFilters(vcfs = hg38.vcfs,
assembly = "hg38",
design = designPanel)
#test_missing(hg38.vcfs_nonfiltered)
# This is the number of variants actually left out after filtering
left_over_count = nrow(hg38.vcfs_nonfiltered$testhg38$variants)
# this is the expected number of variants to be filtered
expected_left_over = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
length()
# Finally run the test
test_that("Test expected number of variants left to be filtered: No Filter", {
expect_equal(left_over_count, expected_left_over)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 1: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes)
hg38.vcfs_NoCancer <-suppressWarnings(applyFilters(vcfs = hg38.vcfs
, assembly="hg38"
, design=designPanel
, remove.cancer=TRUE
, tsList=NULL
, variantType=NULL)
)
#test_missing(hg38.vcfs_NoCancer)
# This is the number of variants actually filtered out
left_over_count = nrow(hg38.vcfs_NoCancer$testhg38$variants)
# this is the expected number of variants to be filtered
expected_left_over = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter", {
expect_equal(left_over_count, expected_left_over)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 2: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and synonymous
# mutations
hg38.vcfs_NoCancer_NoSynonymous <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("synonymous")))
#test_missing(hg38.vcfs_NoCancer_NoSynonymous)
# This is the number of variants actually filtered out
left_over_count = nrow(hg38.vcfs_NoCancer_NoSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + synonimous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 3: remove synonymous mutations
hg38.vcfs_NoSynonymous <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("synonymous"))
#test_missing(hg38.vcfs_NoSynonymous)
left_over_count = nrow(hg38.vcfs_NoSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: synonimous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 4: remove non-synonymous mutations
hg38.vcfs_NoNonSynonymous <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("nonsynonymous"))
#test_missing(hg38.vcfs_NoNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
length()
test_that("Test expected number of variants to be filtered: nonsynonimous ", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 5: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and non-synonymous
# mutations
hg38.vcfs_NoCancerNonSynonymous <-suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsynonymous"))
)
#test_missing(hg38.vcfs_NoCancerNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoCancerNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + nonsynonymous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 6: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and synonymous + non-synonymous
# mutations
hg38.vcfs_NoCancerSynonimousNonSynonymous <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsynonymous", "synonymous"))
)
#test_missing(hg38.vcfs_NoCancerSynonimousNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoCancerSynonimousNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + nonsynonymous + nonsynonymous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 7: remove non-sense mutations
hg38.vcfs_NoNonsense <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("nonsense"))
#test_missing(hg38.vcfs_NoNonsense)
left_over_count = nrow(hg38.vcfs_NoNonsense$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="nonsense") %>%
length()
test_that("Test expected number of variants to be filtered: nonsense", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 8: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and nonsense
# mutations
hg38.vcfs_NoCancerNonsense <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsense"))
)
#test_missing(hg38.vcfs_NoCancerNonsense)
left_over_count = nrow(hg38.vcfs_NoCancerNonsense$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsense") %>%
length()
test_that("Test expected number of variants to be filtered: nonsense + cancer", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 9: remove frameshift mutations
hg38.vcfs_NoFrameshift <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("frameshift"))
#test_missing(hg38.vcfs_NoFrameshift)
left_over_count = nrow(hg38.vcfs_NoFrameshift$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="frameshift") %>%
length()
test_that("Test expected number of variants to be filtered: frameshift", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 10: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and frameshift
# mutations
hg38.vcfs_NoCancerFrameshift <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("frameshift"))
)
#test_missing(hg38.vcfs_NoCancerFrameshift)
left_over_count = nrow(hg38.vcfs_NoCancerFrameshift$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="frameshift") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
length()
test_that("Test expected number of variants to be filtered: frameshift", {
expect_equal(left_over_count, expected_filtered_count)
})
# Filter 11: remove synonymous mutations and mutations with variant allele
# frequency < 0.05
# vcfs_NoSynonymous_VAFFilter <- applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=FALSE,
# tsList=NULL,
# variantType=c("synonymous"))
# # Filter 12: remove mutations with variant allele frequency < 0.05
# vcfs_VAFFilter <- applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=FALSE,
# tsList=NULL,
# variantType=NULL)
#
# Filter 13: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and mutations with
# variant allele frequency < 0.05
# vcfs_NoCancer_VAFFilter <- suppressWarnings(applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=TRUE,
# tsList=NULL,
# variantType=NULL))
# Filter 14: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes), synonymous
# mutations and mutations with variant allele frequency < 0.05
# vcfs_NoCancer_VAFFilter_NoSynonymous <- suppressWarnings(applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=TRUE,
# tsList=NULL,
# variantType=c("synonymous")))
################################################################################
# TESTS
################################################################################
# TEST WRONG INPUT FORMAT
# ------------------------------------------------------------------------------
test_that("test wrong input: hg38.vcfs", {
# missing entry
expect_error(
applyFilters(assembly = "hg38", design = design_gr)
, "argument \"vcfs\" is missing, with no default"
)
# Object does not exists
expect_error(
applyFilters(vcfs = banana_vcfs, assembly = "hg38", design = designPanel)
, "object 'banana_vcfs' not found", fixed=TRUE
)
})
test_that("test expect wrong input: assembly", {
# missing entry
expect_error(
applyFilters(vcfs = hg38.vcfs, design = designPanel)
, "argument \"assembly\" is missing, with no default"
)
# wrong entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "banana", design = designPanel)
, "No valid genome assembly: please specify 'hg19' or 'hg38'"
)
})
test_that("test wrong input: design", {
# missing entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38")
, "argument \"design\" is missing, with no default"
)
# Object does not exists
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designBanana)
, "object 'designBanana' not found", fixed=TRUE
)
})
test_that("test wrong input: vaf.cutoff", {
# wrong format entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = "ciao", remove.cancer = FALSE, tsList = NULL, variantType = NULL)
, "vaf.cutoff should be numeric type"
)
# wrong range value entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = 30)
, "vaf.cutoff can't be higher than 1"
)
})
test_that("test input: vaf.cutoff", {
# wrong format entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = NULL)
, "vaf.cutoff should be numeric type"
)
})
# TEST OUTPUT FORMAT FROM THE FILTER
# ----------------------------------------------------------------
# make sure the output from the filter is in the correct format and consistent
test_that("Class of function output corresponds to the expected one", {
expect_is(hg38.vcfs_nonfiltered, "list")
expect_is(hg38.vcfs_NoCancer, "list")
expect_is(hg38.vcfs_NoCancer[[1]], "list")
expect_is(hg38.vcfs_NoCancer[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoCancer[[1]]$filter, "character")
expect_is(hg38.vcfs_NoCancer[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoCancer[[1]]$sample, "character")
expect_is(hg38.vcfs_NoCancer_NoSynonymous, "list")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]], "list")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$filter, "character")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$sample, "character")
expect_is(hg38.vcfs_NoSynonymous, "list")
expect_is(hg38.vcfs_NoSynonymous[[1]], "list")
expect_is(hg38.vcfs_NoSynonymous[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoSynonymous[[1]]$filter, "character")
expect_is(hg38.vcfs_NoSynonymous[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoSynonymous[[1]]$sample, "character")
# expect_is(vcfs_NoSynonymous_VAFFilter, "list")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]], "list")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_VAFFilter, "list")
# expect_is(vcfs_VAFFilter[[1]], "list")
# expect_is(vcfs_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_NoCancer_VAFFilter, "list")
# expect_is(vcfs_NoCancer_VAFFilter[[1]], "list")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous, "list")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]], "list")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$variants, "data.frame")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$filter, "character")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$design, "GRanges")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$sample, "character")
})
## Test dimensions of output objects from functions ##
test_that("Number of variants generated in output by applyFilter function is not higher than number of variants in input", {
# Compare n variants in input expanded VCF object and in output dataframe
extraction <- hg38.vcfs[[1]] %>%
S4Vectors::expand() %>%
SummarizedExperiment::rowRanges() %>%
length()
expect_true(extraction >= dim(hg38.vcfs_NoCancer[[1]]$variants)[1])
expect_true(extraction >= dim(hg38.vcfs_NoCancer_NoSynonymous[[1]]$variants)[1])
expect_true(extraction >= dim(hg38.vcfs_NoSynonymous[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoSynonymous_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoCancer_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$variants)[1])
})
test_that("Dimensions of function output correspond to the expected ones", {
# Number of elements in lists generated by applyFilters
expect_equal(length(hg38.vcfs_NoCancer[[1]]), 4)
expect_equal(length(hg38.vcfs_NoCancer_NoSynonymous[[1]]), 4)
expect_equal(length(hg38.vcfs_NoSynonymous[[1]]), 4)
# expect_equal(length(vcfs_NoSynonymous_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]), 4)
})
test_that("Number of variants filtered correspond to the expected ones", {
# Number of elements in lists generated by applyFilters
expect_equal(nrow(hg38.vcfs_nonfiltered[[1]][["variants"]]), 31)
expect_equal(nrow(hg38.vcfs_NoCancer[[1]][["variants"]]), 14)
expect_equal(nrow(hg38.vcfs_NoCancer_NoSynonymous[[1]][["variants"]]), 7)
expect_equal(nrow(hg38.vcfs_NoSynonymous[[1]][["variants"]]), 24)
expect_equal(nrow(hg38.vcfs_NoNonSynonymous[[1]][["variants"]]), 23)
expect_equal(nrow(hg38.vcfs_NoCancerNonSynonymous[[1]][["variants"]]), 7)
expect_equal(nrow(hg38.vcfs_NoCancerSynonimousNonSynonymous[[1]][["variants"]]), 0)
expect_equal(nrow(hg38.vcfs_NoNonsense[[1]][["variants"]]), 22)
expect_equal(nrow(hg38.vcfs_NoCancerNonsense[[1]][["variants"]]), 14)
expect_equal(nrow(hg38.vcfs_NoFrameshift[[1]][["variants"]]), 27)
expect_equal(nrow(hg38.vcfs_NoCancerFrameshift[[1]][["variants"]]), 14)
# expect_equal(length(vcfs_NoSynonymous_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]), 4)
})
context("applyTMB.R")
TMB_vcfs0=applyTMB(inputForTMB = hg38.vcfs_nonfiltered, assembly = "hg38")
TMB_vcfs1=applyTMB(inputForTMB = hg38.vcfs_NoCancer, assembly = "hg38")
TMB_vcfs2=applyTMB(inputForTMB = hg38.vcfs_NoCancer_NoSynonymous, assembly = "hg38")
TMB_vcfs3=applyTMB(inputForTMB = hg38.vcfs_NoSynonymous, assembly = "hg38")
TMB_vcfs4=applyTMB(inputForTMB = hg38.vcfs_NoNonSynonymous, assembly = "hg38")
TMB_vcfs5=applyTMB(inputForTMB = hg38.vcfs_NoCancerNonSynonymous, assembly = "hg38")
TMB_vcfs6=applyTMB(inputForTMB = hg38.vcfs_NoCancerSynonimousNonSynonymous, assembly = "hg38")
TMB_vcfs7=applyTMB(inputForTMB = hg38.vcfs_NoNonsense, assembly = "hg38")
TMB_vcfs8=applyTMB(inputForTMB = hg38.vcfs_NoCancerNonsense, assembly = "hg38")
TMB_vcfs9=applyTMB(inputForTMB = hg38.vcfs_NoFrameshift, assembly = "hg38")
TMB_vcfs10=applyTMB(inputForTMB = hg38.vcfs_NoCancerFrameshift, assembly = "hg38")
# TMB_vcfs11=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs12=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs13=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs14=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TESTS ON OUTPUT #
## Test class of output objects from functions ##
test_that("Class of function output corresponds to the expected one", {
expect_is(TMB_vcfs0, "data.frame")
# expect_is(TMB_vcfs$Sample, "factor")
# expect_is(TMB_vcfs$Filter, "factor")
expect_is(TMB_vcfs0$Sequencing_Size, "numeric")
expect_is(TMB_vcfs0$Tot_Number_Mutations, "numeric")
expect_is(TMB_vcfs0$TMB_per_Mb, "numeric")
})
test_that("Dimensions of function output correspond to the expected ones", {
expect_equal(dim(TMB_vcfs0)[1], 1)
expect_equal(dim(TMB_vcfs0)[2], 6)
})
test_that("TMB results correspond to the expected ones", {
expect_equal(TMB_vcfs0$TMB_per_Mb,0.19)
expect_equal(TMB_vcfs1$TMB_per_Mb,0.09)
expect_equal(TMB_vcfs2$TMB_per_Mb,0.04)
expect_equal(TMB_vcfs3$TMB_per_Mb,0.15)
expect_equal(TMB_vcfs4$TMB_per_Mb,0.14)
expect_equal(TMB_vcfs5$TMB_per_Mb,0.04)
expect_equal(TMB_vcfs6$TMB_per_Mb,0.00)
expect_equal(TMB_vcfs7$TMB_per_Mb,0.14)
expect_equal(TMB_vcfs8$TMB_per_Mb,0.09)
expect_equal(TMB_vcfs9$TMB_per_Mb,0.17)
expect_equal(TMB_vcfs10$TMB_per_Mb,0.09)
# expect_equal(TMB_vcfs11$TMB_per_Mb,0)
# expect_equal(TMB_vcfs12$TMB_per_Mb,0)
# expect_equal(TMB_vcfs13$TMB_per_Mb,0)
# expect_equal(TMB_vcfs14$TMB_per_Mb,0)
})
acc-bioinfo/TMBleR documentation built on Dec. 18, 2021, 10:21 p.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.
context("applyFilters_hg38.R")
################################################################################
# Helper function
################################################################################
test_missing <- function(x)
{
" Check the number of variants (filtered + passed) is equal to those evaluated by the filter (input vcf) "
if(isFALSE(debug_env$debug)){
print("Set debug_env$debug = TRUE in '/R/globalVariable.R'")
debug_env$debug = TRUE
}
passed.var <- x[[1]][[1]] %>% nrow
filtered.var <- debug_env$filters %>% nrow
input.var <- hg38.vcfs[[1]]@fixed %>% nrow
list(cat("Filtered:", filtered.var
,"\nPassed:", passed.var
,"\nInput Variants:", input.var
,"\nmissing:", input.var - sum(filtered.var, passed.var)))
expect_true( input.var == sum(filtered.var, passed.var) )
}
# Conditions:
# 1. Set debug_env$debug = TRUE
# 2. Launch only after the corresponding filter
#test_missing(hg38.vcfs_nonfiltered)
#test_missing(hg38.vcfs_NoCancer)
# Helper fn to check in the vcf file if the FILTER field contains the expected match
# in the original vcf file used as input. If returns the the FILTER field without the
# expected match
find_expected_filter_type <- function(variant_vector=hg38.vcfs$testhg38@fixed$FILTER, expected_filter_type){
idx_filter <- purrr::map_lgl(variant_vector, ~ {
out <- unlist(strsplit(.x,";", fixed = TRUE))
out <- unlist(strsplit(out, "="))
out <- unlist(strsplit(out, "|", fixed=TRUE))
out <- out == expected_filter_type
return(any(out))
})
return(variant_vector[!idx_filter])
}
################################################################################
# PREPARATION
################################################################################
# Define vcf path and read in vcf files
hg38.vcf_files <- list(testhg38= system.file("extdata", "hg38.test.vcf", package = "TMBleR", mustWork = TRUE))
hg38.vcfs <- readVcfFiles(hg38.vcf_files, assembly = "hg38")
# Read in input the panel sequencing design
designPanel <- readDesign(system.file("extdata"
, "ExamplePanel_design_OnlyChr7ForTest_hg38.bed"
, package = "TMBleR"
, mustWork = TRUE)
, assembly = "hg38")
# ------------------------------------------------------------------------------
# Apply different filters
# ------------------------------------------------------------------------------
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 0: no filters - only filtered due to .bed file & intronic regions
hg38.vcfs_nonfiltered <- applyFilters(vcfs = hg38.vcfs,
assembly = "hg38",
design = designPanel)
#test_missing(hg38.vcfs_nonfiltered)
# This is the number of variants actually left out after filtering
left_over_count = nrow(hg38.vcfs_nonfiltered$testhg38$variants)
# this is the expected number of variants to be filtered
expected_left_over = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
length()
# Finally run the test
test_that("Test expected number of variants left to be filtered: No Filter", {
expect_equal(left_over_count, expected_left_over)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 1: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes)
hg38.vcfs_NoCancer <-suppressWarnings(applyFilters(vcfs = hg38.vcfs
, assembly="hg38"
, design=designPanel
, remove.cancer=TRUE
, tsList=NULL
, variantType=NULL)
)
#test_missing(hg38.vcfs_NoCancer)
# This is the number of variants actually filtered out
left_over_count = nrow(hg38.vcfs_NoCancer$testhg38$variants)
# this is the expected number of variants to be filtered
expected_left_over = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter", {
expect_equal(left_over_count, expected_left_over)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 2: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and synonymous
# mutations
hg38.vcfs_NoCancer_NoSynonymous <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("synonymous")))
#test_missing(hg38.vcfs_NoCancer_NoSynonymous)
# This is the number of variants actually filtered out
left_over_count = nrow(hg38.vcfs_NoCancer_NoSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + synonimous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 3: remove synonymous mutations
hg38.vcfs_NoSynonymous <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("synonymous"))
#test_missing(hg38.vcfs_NoSynonymous)
left_over_count = nrow(hg38.vcfs_NoSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: synonimous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 4: remove non-synonymous mutations
hg38.vcfs_NoNonSynonymous <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("nonsynonymous"))
#test_missing(hg38.vcfs_NoNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
length()
test_that("Test expected number of variants to be filtered: nonsynonimous ", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 5: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and non-synonymous
# mutations
hg38.vcfs_NoCancerNonSynonymous <-suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsynonymous"))
)
#test_missing(hg38.vcfs_NoCancerNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoCancerNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + nonsynonymous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 6: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and synonymous + non-synonymous
# mutations
hg38.vcfs_NoCancerSynonimousNonSynonymous <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsynonymous", "synonymous"))
)
#test_missing(hg38.vcfs_NoCancerSynonimousNonSynonymous)
left_over_count = nrow(hg38.vcfs_NoCancerSynonimousNonSynonymous$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsynonimous") %>%
find_expected_filter_type(expected_filter_type="synonimous") %>%
length()
test_that("Test expected number of variants to be filtered: Cancer Filter + nonsynonymous + nonsynonymous", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 7: remove non-sense mutations
hg38.vcfs_NoNonsense <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("nonsense"))
#test_missing(hg38.vcfs_NoNonsense)
left_over_count = nrow(hg38.vcfs_NoNonsense$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="nonsense") %>%
length()
test_that("Test expected number of variants to be filtered: nonsense", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 8: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and nonsense
# mutations
hg38.vcfs_NoCancerNonsense <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("nonsense"))
)
#test_missing(hg38.vcfs_NoCancerNonsense)
left_over_count = nrow(hg38.vcfs_NoCancerNonsense$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
find_expected_filter_type(expected_filter_type="nonsense") %>%
length()
test_that("Test expected number of variants to be filtered: nonsense + cancer", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 9: remove frameshift mutations
hg38.vcfs_NoFrameshift <- applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=FALSE,
tsList=NULL,
variantType=c("frameshift"))
#test_missing(hg38.vcfs_NoFrameshift)
left_over_count = nrow(hg38.vcfs_NoFrameshift$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="frameshift") %>%
length()
test_that("Test expected number of variants to be filtered: frameshift", {
expect_equal(left_over_count, expected_filtered_count)
})
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
# Filter 10: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and frameshift
# mutations
hg38.vcfs_NoCancerFrameshift <- suppressWarnings(applyFilters(vcfs = hg38.vcfs,
assembly="hg38",
design=designPanel,
remove.cancer=TRUE,
tsList=NULL,
variantType=c("frameshift"))
)
#test_missing(hg38.vcfs_NoCancerFrameshift)
left_over_count = nrow(hg38.vcfs_NoCancerFrameshift$testhg38$variants)
# this is the expected number of variants to be filtered
expected_filtered_count = find_expected_filter_type(expected_filter_type="off_target") %>%
find_expected_filter_type(expected_filter_type="non_coding") %>%
find_expected_filter_type(expected_filter_type="frameshift") %>%
find_expected_filter_type(expected_filter_type="cancer") %>%
length()
test_that("Test expected number of variants to be filtered: frameshift", {
expect_equal(left_over_count, expected_filtered_count)
})
# Filter 11: remove synonymous mutations and mutations with variant allele
# frequency < 0.05
# vcfs_NoSynonymous_VAFFilter <- applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=FALSE,
# tsList=NULL,
# variantType=c("synonymous"))
# # Filter 12: remove mutations with variant allele frequency < 0.05
# vcfs_VAFFilter <- applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=FALSE,
# tsList=NULL,
# variantType=NULL)
#
# Filter 13: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes) and mutations with
# variant allele frequency < 0.05
# vcfs_NoCancer_VAFFilter <- suppressWarnings(applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=TRUE,
# tsList=NULL,
# variantType=NULL))
# Filter 14: remove known cancer mutations (e.g. coding mutations described in
# COSMIC and truncating mutations in tumor suppressor genes), synonymous
# mutations and mutations with variant allele frequency < 0.05
# vcfs_NoCancer_VAFFilter_NoSynonymous <- suppressWarnings(applyFilters(vcfs,
# assembly="hg19",
# design=designPanel,
# vaf.cutoff=0.05,
# remove.cancer=TRUE,
# tsList=NULL,
# variantType=c("synonymous")))
################################################################################
# TESTS
################################################################################
# TEST WRONG INPUT FORMAT
# ------------------------------------------------------------------------------
test_that("test wrong input: hg38.vcfs", {
# missing entry
expect_error(
applyFilters(assembly = "hg38", design = design_gr)
, "argument \"vcfs\" is missing, with no default"
)
# Object does not exists
expect_error(
applyFilters(vcfs = banana_vcfs, assembly = "hg38", design = designPanel)
, "object 'banana_vcfs' not found", fixed=TRUE
)
})
test_that("test expect wrong input: assembly", {
# missing entry
expect_error(
applyFilters(vcfs = hg38.vcfs, design = designPanel)
, "argument \"assembly\" is missing, with no default"
)
# wrong entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "banana", design = designPanel)
, "No valid genome assembly: please specify 'hg19' or 'hg38'"
)
})
test_that("test wrong input: design", {
# missing entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38")
, "argument \"design\" is missing, with no default"
)
# Object does not exists
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designBanana)
, "object 'designBanana' not found", fixed=TRUE
)
})
test_that("test wrong input: vaf.cutoff", {
# wrong format entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = "ciao", remove.cancer = FALSE, tsList = NULL, variantType = NULL)
, "vaf.cutoff should be numeric type"
)
# wrong range value entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = 30)
, "vaf.cutoff can't be higher than 1"
)
})
test_that("test input: vaf.cutoff", {
# wrong format entry
expect_error(
applyFilters(vcfs = hg38.vcfs, assembly = "hg38", design = designPanel, vaf.cutoff = NULL)
, "vaf.cutoff should be numeric type"
)
})
# TEST OUTPUT FORMAT FROM THE FILTER
# ----------------------------------------------------------------
# make sure the output from the filter is in the correct format and consistent
test_that("Class of function output corresponds to the expected one", {
expect_is(hg38.vcfs_nonfiltered, "list")
expect_is(hg38.vcfs_NoCancer, "list")
expect_is(hg38.vcfs_NoCancer[[1]], "list")
expect_is(hg38.vcfs_NoCancer[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoCancer[[1]]$filter, "character")
expect_is(hg38.vcfs_NoCancer[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoCancer[[1]]$sample, "character")
expect_is(hg38.vcfs_NoCancer_NoSynonymous, "list")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]], "list")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$filter, "character")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoCancer_NoSynonymous[[1]]$sample, "character")
expect_is(hg38.vcfs_NoSynonymous, "list")
expect_is(hg38.vcfs_NoSynonymous[[1]], "list")
expect_is(hg38.vcfs_NoSynonymous[[1]]$variants, "data.frame")
expect_is(hg38.vcfs_NoSynonymous[[1]]$filter, "character")
expect_is(hg38.vcfs_NoSynonymous[[1]]$design, "GRanges")
expect_is(hg38.vcfs_NoSynonymous[[1]]$sample, "character")
# expect_is(vcfs_NoSynonymous_VAFFilter, "list")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]], "list")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_NoSynonymous_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_VAFFilter, "list")
# expect_is(vcfs_VAFFilter[[1]], "list")
# expect_is(vcfs_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_NoCancer_VAFFilter, "list")
# expect_is(vcfs_NoCancer_VAFFilter[[1]], "list")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$variants, "data.frame")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$filter, "character")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$design, "GRanges")
# expect_is(vcfs_NoCancer_VAFFilter[[1]]$sample, "character")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous, "list")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]], "list")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$variants, "data.frame")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$filter, "character")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$design, "GRanges")
# expect_is(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$sample, "character")
})
## Test dimensions of output objects from functions ##
test_that("Number of variants generated in output by applyFilter function is not higher than number of variants in input", {
# Compare n variants in input expanded VCF object and in output dataframe
extraction <- hg38.vcfs[[1]] %>%
S4Vectors::expand() %>%
SummarizedExperiment::rowRanges() %>%
length()
expect_true(extraction >= dim(hg38.vcfs_NoCancer[[1]]$variants)[1])
expect_true(extraction >= dim(hg38.vcfs_NoCancer_NoSynonymous[[1]]$variants)[1])
expect_true(extraction >= dim(hg38.vcfs_NoSynonymous[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoSynonymous_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoCancer_VAFFilter[[1]]$variants)[1])
# expect_true(extraction >= dim(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]$variants)[1])
})
test_that("Dimensions of function output correspond to the expected ones", {
# Number of elements in lists generated by applyFilters
expect_equal(length(hg38.vcfs_NoCancer[[1]]), 4)
expect_equal(length(hg38.vcfs_NoCancer_NoSynonymous[[1]]), 4)
expect_equal(length(hg38.vcfs_NoSynonymous[[1]]), 4)
# expect_equal(length(vcfs_NoSynonymous_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]), 4)
})
test_that("Number of variants filtered correspond to the expected ones", {
# Number of elements in lists generated by applyFilters
expect_equal(nrow(hg38.vcfs_nonfiltered[[1]][["variants"]]), 31)
expect_equal(nrow(hg38.vcfs_NoCancer[[1]][["variants"]]), 14)
expect_equal(nrow(hg38.vcfs_NoCancer_NoSynonymous[[1]][["variants"]]), 7)
expect_equal(nrow(hg38.vcfs_NoSynonymous[[1]][["variants"]]), 24)
expect_equal(nrow(hg38.vcfs_NoNonSynonymous[[1]][["variants"]]), 23)
expect_equal(nrow(hg38.vcfs_NoCancerNonSynonymous[[1]][["variants"]]), 7)
expect_equal(nrow(hg38.vcfs_NoCancerSynonimousNonSynonymous[[1]][["variants"]]), 0)
expect_equal(nrow(hg38.vcfs_NoNonsense[[1]][["variants"]]), 22)
expect_equal(nrow(hg38.vcfs_NoCancerNonsense[[1]][["variants"]]), 14)
expect_equal(nrow(hg38.vcfs_NoFrameshift[[1]][["variants"]]), 27)
expect_equal(nrow(hg38.vcfs_NoCancerFrameshift[[1]][["variants"]]), 14)
# expect_equal(length(vcfs_NoSynonymous_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter[[1]]), 4)
# expect_equal(length(vcfs_NoCancer_VAFFilter_NoSynonymous[[1]]), 4)
})
context("applyTMB.R")
TMB_vcfs0=applyTMB(inputForTMB = hg38.vcfs_nonfiltered, assembly = "hg38")
TMB_vcfs1=applyTMB(inputForTMB = hg38.vcfs_NoCancer, assembly = "hg38")
TMB_vcfs2=applyTMB(inputForTMB = hg38.vcfs_NoCancer_NoSynonymous, assembly = "hg38")
TMB_vcfs3=applyTMB(inputForTMB = hg38.vcfs_NoSynonymous, assembly = "hg38")
TMB_vcfs4=applyTMB(inputForTMB = hg38.vcfs_NoNonSynonymous, assembly = "hg38")
TMB_vcfs5=applyTMB(inputForTMB = hg38.vcfs_NoCancerNonSynonymous, assembly = "hg38")
TMB_vcfs6=applyTMB(inputForTMB = hg38.vcfs_NoCancerSynonimousNonSynonymous, assembly = "hg38")
TMB_vcfs7=applyTMB(inputForTMB = hg38.vcfs_NoNonsense, assembly = "hg38")
TMB_vcfs8=applyTMB(inputForTMB = hg38.vcfs_NoCancerNonsense, assembly = "hg38")
TMB_vcfs9=applyTMB(inputForTMB = hg38.vcfs_NoFrameshift, assembly = "hg38")
TMB_vcfs10=applyTMB(inputForTMB = hg38.vcfs_NoCancerFrameshift, assembly = "hg38")
# TMB_vcfs11=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs12=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs13=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TMB_vcfs14=applyTMB(inputForTMB = vcfs_NoCancer, assembly = "hg19")
# TESTS ON OUTPUT #
## Test class of output objects from functions ##
test_that("Class of function output corresponds to the expected one", {
expect_is(TMB_vcfs0, "data.frame")
# expect_is(TMB_vcfs$Sample, "factor")
# expect_is(TMB_vcfs$Filter, "factor")
expect_is(TMB_vcfs0$Sequencing_Size, "numeric")
expect_is(TMB_vcfs0$Tot_Number_Mutations, "numeric")
expect_is(TMB_vcfs0$TMB_per_Mb, "numeric")
})
test_that("Dimensions of function output correspond to the expected ones", {
expect_equal(dim(TMB_vcfs0)[1], 1)
expect_equal(dim(TMB_vcfs0)[2], 6)
})
test_that("TMB results correspond to the expected ones", {
expect_equal(TMB_vcfs0$TMB_per_Mb,0.19)
expect_equal(TMB_vcfs1$TMB_per_Mb,0.09)
expect_equal(TMB_vcfs2$TMB_per_Mb,0.04)
expect_equal(TMB_vcfs3$TMB_per_Mb,0.15)
expect_equal(TMB_vcfs4$TMB_per_Mb,0.14)
expect_equal(TMB_vcfs5$TMB_per_Mb,0.04)
expect_equal(TMB_vcfs6$TMB_per_Mb,0.00)
expect_equal(TMB_vcfs7$TMB_per_Mb,0.14)
expect_equal(TMB_vcfs8$TMB_per_Mb,0.09)
expect_equal(TMB_vcfs9$TMB_per_Mb,0.17)
expect_equal(TMB_vcfs10$TMB_per_Mb,0.09)
# expect_equal(TMB_vcfs11$TMB_per_Mb,0)
# expect_equal(TMB_vcfs12$TMB_per_Mb,0)
# expect_equal(TMB_vcfs13$TMB_per_Mb,0)
# expect_equal(TMB_vcfs14$TMB_per_Mb,0)
})
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.