From 27a4af4cac24c3adcfd0bfd0283a26517ac2df0f Mon Sep 17 00:00:00 2001
From: aduvermy <arnaud.duvermy@ens-lyon.fr>
Date: Tue, 30 Jan 2024 09:11:01 +0100
Subject: [PATCH] fix error DESeq - too small counts simulated
---
R/simulation_report.R | 1 -
dev/flat_full.Rmd | 4 +++-
tests/testthat/test-simulation_report.R | 4 +++-
3 files changed, 6 insertions(+), 3 deletions(-)
diff --git a/R/simulation_report.R b/R/simulation_report.R
index ddff120..c3548f0 100644
--- a/R/simulation_report.R
+++ b/R/simulation_report.R
@@ -247,7 +247,6 @@ compute_metrics_summary <- function(dt) {
#' @return A list containing separate data frames for classification metrics by parameter value
#' and for aggregated classification metrics.
#'
-#' @examples
#' @importFrom data.table setDT .SD
#' @export
get_ml_metrics_obj <- function(evaldata_params, alpha_risk = 0.05, col_param = "description"){
diff --git a/dev/flat_full.Rmd b/dev/flat_full.Rmd
index a37c57a..3ea6f7b 100644
--- a/dev/flat_full.Rmd
+++ b/dev/flat_full.Rmd
@@ -8246,13 +8246,15 @@ test_that("rbind_evaldata_tmb_dds returns correct output", {
N_GENES = 15
MIN_REPLICATES = 3
MAX_REPLICATES = 3
+ BASAL_EXPR <- 3
########################
## -- simulate RNAseq data based on input_var_list, minimum input required
## -- number of replicate randomly defined between MIN_REP and MAX_REP
mock_data <- mock_rnaseq(input_var_list, N_GENES,
min_replicates = MIN_REPLICATES,
- max_replicates = MAX_REPLICATES)
+ max_replicates = MAX_REPLICATES,
+ basal_expression = BASAL_EXPR)
## -- data from simulation
count_matrix <- mock_data$counts
metaData <- mock_data$metadata
diff --git a/tests/testthat/test-simulation_report.R b/tests/testthat/test-simulation_report.R
index 822e642..4f06316 100644
--- a/tests/testthat/test-simulation_report.R
+++ b/tests/testthat/test-simulation_report.R
@@ -220,13 +220,15 @@ test_that("rbind_evaldata_tmb_dds returns correct output", {
N_GENES = 15
MIN_REPLICATES = 3
MAX_REPLICATES = 3
+ BASAL_EXPR <- 3
########################
## -- simulate RNAseq data based on input_var_list, minimum input required
## -- number of replicate randomly defined between MIN_REP and MAX_REP
mock_data <- mock_rnaseq(input_var_list, N_GENES,
min_replicates = MIN_REPLICATES,
- max_replicates = MAX_REPLICATES)
+ max_replicates = MAX_REPLICATES,
+ basal_expression = BASAL_EXPR)
## -- data from simulation
count_matrix <- mock_data$counts
metaData <- mock_data$metadata
--
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