Merge pull request #351 from biomage-org/hotfix-genes-v-umi

HOTFIX: genes v umi filter not using user-defined parameters
hms-dbmi-cellenics · Jan 4, 2024 · 47aaa32 · 47aaa32
2 parents 993ebc4 + 3368b7b
commit 47aaa32
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diff --git a/pipeline-runner/R/qc-4-filter_gene_umi_outlier.R b/pipeline-runner/R/qc-4-filter_gene_umi_outlier.R
@@ -55,7 +55,7 @@ filter_gene_umi_outlier <- function(scdata_list, config, sample_id, cells_id, ta
   if (safeTRUE(config$auto))
     p_level <- min(0.001, 1 / ncol(sample_data))
   else
-    p_level <- config$filterSettings$regressionTypeSettings[[type]]$p.level
+    p_level <- 1 - as.numeric(config$filterSettings$predictionInterval)
 
   p_level <- suppressWarnings(as.numeric(p_level))
   if(is.na(p_level)) stop("p_level couldn't be interpreted as a number.")

diff --git a/pipeline-runner/tests/testthat/test-qc-4-filter_gene_umi_outlier.R b/pipeline-runner/tests/testthat/test-qc-4-filter_gene_umi_outlier.R
@@ -164,6 +164,7 @@ test_that("Gene UMI filter works if input is a a float-interpretable string", {
   cells_id <- mock_ids()
   nstart <- ncol(scdata_list[[sample_2_id]])
   config$auto <- FALSE
+  config$filterSettings$predictionInterval <- "0.3"
 
   out_number <- filter_gene_umi_outlier(scdata_list, config, sample_2_id, cells_id)