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update test
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@kevinlkx
kevinlkx committed Jul 23, 2024
1 parent c952356 commit 7230031
Showing 1 changed file with 55 additions and 55 deletions.
110 changes: 55 additions & 55 deletions tests/testthat/test-ctwas_merge_regions.R
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,7 @@ test_that("merge_region_data works", {
boundary_genes <- ctwas_res$boundary_genes
region_data <- ctwas_res$region_data

precomputed_merged_region_data <- readRDS(system.file("tests/testthat", "LDL_example.merged_region_data.RDS", package = "ctwas"))
precomputed_merged_region_data <- readRDS("LDL_example.merged_region_data.RDS")

capture.output({
res <- merge_region_data(boundary_genes,
Expand Down Expand Up @@ -45,8 +45,8 @@ test_that("merge_region_data and finemapping without LD works", {
group_prior <- ctwas_res$param$group_prior
group_prior_var <- ctwas_res$param$group_prior_var

precomputed_merged_region_data <- readRDS(system.file("tests/testthat", "LDL_example.merged_region_data.RDS", package = "ctwas"))
precomputed_finemap_merged_regions_res <- readRDS(system.file("tests/testthat", "LDL_example.finemap_merged_regions_noLD_res.RDS", package = "ctwas"))
precomputed_merged_region_data <- readRDS("LDL_example.merged_region_data.RDS")
precomputed_finemap_merged_regions_res <- readRDS("LDL_example.finemap_merged_regions_noLD_res.RDS")

capture.output({
res <- merge_region_data(boundary_genes,
Expand All @@ -73,55 +73,55 @@ test_that("merge_region_data and finemapping without LD works", {

})

test_that("merge_region_data and finemapping with LD works", {

LD_map <- readRDS(system.file("extdata/sample_data", "LDL_example.LD_map.RDS", package = "ctwas"))
skip_if_no_LD_file(LD_map$LD_file)

z_snp <- readRDS(system.file("extdata/sample_data", "LDL_example.preprocessed.z_snp.RDS", package = "ctwas"))
weights <- readRDS(system.file("extdata/sample_data", "LDL_example.preprocessed.weights.RDS", package = "ctwas"))
region_info <- readRDS(system.file("extdata/sample_data", "LDL_example.region_info.RDS", package = "ctwas"))
snp_map <- readRDS(system.file("extdata/sample_data", "LDL_example.snp_map.RDS", package = "ctwas"))
ctwas_res <- readRDS(system.file("extdata/sample_data", "LDL_example.ctwas_sumstats_res.RDS", package = "ctwas"))
z_gene <- ctwas_res$z_gene
boundary_genes <- ctwas_res$boundary_genes
region_data <- ctwas_res$region_data
group_prior <- ctwas_res$param$group_prior
group_prior_var <- ctwas_res$param$group_prior_var

precomputed_merged_region_data <- readRDS(system.file("tests/testthat", "LDL_example.merged_region_data.RDS", package = "ctwas"))
precomputed_finemap_merged_regions_res <- readRDS(system.file("tests/testthat", "LDL_example.finemap_merged_regions_res.RDS", package = "ctwas"))

capture.output({
res <- merge_region_data(boundary_genes,
region_data,
region_info = region_info,
snp_map = snp_map,
LD_map = LD_map,
weights = weights,
z_snp = z_snp,
z_gene = z_gene,
use_LD = TRUE,
estimate_L = TRUE,
maxSNP = 20000)
merged_region_data <- res$merged_region_data
merged_region_info <- res$merged_region_info
merged_LD_map <- res$merged_LD_map
merged_snp_map <- res$merged_snp_map
merged_region_id_map <- res$merged_region_id_map
merged_region_L <- res$merged_region_L

finemap_merged_regions_res <- finemap_regions(merged_region_data,
use_LD = TRUE,
LD_map = merged_LD_map,
snp_map = merged_snp_map,
weights = weights,
group_prior = group_prior,
group_prior_var = group_prior_var,
L = merged_region_L)
})

expect_equal(merged_region_data, precomputed_merged_region_data)
expect_equal(finemap_merged_regions_res, precomputed_finemap_merged_regions_res)

})
# test_that("merge_region_data and finemapping with LD works", {
#
# LD_map <- readRDS(system.file("extdata/sample_data", "LDL_example.LD_map.RDS", package = "ctwas"))
# skip_if_no_LD_file(LD_map$LD_file)
#
# z_snp <- readRDS(system.file("extdata/sample_data", "LDL_example.preprocessed.z_snp.RDS", package = "ctwas"))
# weights <- readRDS(system.file("extdata/sample_data", "LDL_example.preprocessed.weights.RDS", package = "ctwas"))
# region_info <- readRDS(system.file("extdata/sample_data", "LDL_example.region_info.RDS", package = "ctwas"))
# snp_map <- readRDS(system.file("extdata/sample_data", "LDL_example.snp_map.RDS", package = "ctwas"))
# ctwas_res <- readRDS(system.file("extdata/sample_data", "LDL_example.ctwas_sumstats_res.RDS", package = "ctwas"))
# z_gene <- ctwas_res$z_gene
# boundary_genes <- ctwas_res$boundary_genes
# region_data <- ctwas_res$region_data
# group_prior <- ctwas_res$param$group_prior
# group_prior_var <- ctwas_res$param$group_prior_var
#
# precomputed_merged_region_data <- readRDS("LDL_example.merged_region_data.RDS")
# precomputed_finemap_merged_regions_res <- readRDS("LDL_example.finemap_merged_regions_res.RDS")
#
# capture.output({
# res <- merge_region_data(boundary_genes,
# region_data,
# region_info = region_info,
# snp_map = snp_map,
# LD_map = LD_map,
# weights = weights,
# z_snp = z_snp,
# z_gene = z_gene,
# use_LD = TRUE,
# estimate_L = TRUE,
# maxSNP = 20000)
# merged_region_data <- res$merged_region_data
# merged_region_info <- res$merged_region_info
# merged_LD_map <- res$merged_LD_map
# merged_snp_map <- res$merged_snp_map
# merged_region_id_map <- res$merged_region_id_map
# merged_region_L <- res$merged_region_L
#
# finemap_merged_regions_res <- finemap_regions(merged_region_data,
# use_LD = TRUE,
# LD_map = merged_LD_map,
# snp_map = merged_snp_map,
# weights = weights,
# group_prior = group_prior,
# group_prior_var = group_prior_var,
# L = merged_region_L)
# })
#
# expect_equal(merged_region_data, precomputed_merged_region_data)
# expect_equal(finemap_merged_regions_res, precomputed_finemap_merged_regions_res)
#
# })

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