Refactor filtering method to be case-insensitive

R/filter_cells.R

@@ -40,7 +40,8 @@ filter_cells <- function(
 ) {
   nFeature_RNA <- NULL
   so_filt <- BiocGenerics::subset(so, subset = nFeature_RNA > 200) # standard low cell read filter
-  if (method == "miQC") {
+  so_qc <- so_filt
+  if (grepl(pattern = "miQC", x = method, ignore.case = TRUE)) {
     print("--filtering cells with miQC")
 
     so_qc <- SeuratWrappers::RunMiQC(
@@ -51,8 +52,7 @@ filter_cells <- function(
       model.slot = "flexmix_model"
     )
     so_qc$keep <- so_qc$miQC.keep
-  } else if (method == "manual") {
-    so_qc <- so_filt
+  } else if (grepl(pattern = "manual", x = method, ignore.case = TRUE)) {
     so_qc$keep <- "discard"
     so_qc$keep[which(
       so_qc$nCount_RNA <= nCount_RNA_max &
@@ -62,8 +62,7 @@ filter_cells <- function(
         so_qc$percent.mt <= percent_mt_max &
         so_qc$percent.mt >= percent_mt_min
     )] <- "keep"
-  } else if (method == "mads") {
-    so_qc <- so_filt
+  } else if (grepl(pattern = "mads", x = method, ignore.case = TRUE)) {
     nCount_out <- Routliers::outliers_mad(
       so_qc$nCount_RNA,
       threshold = mads
@@ -82,6 +81,11 @@ filter_cells <- function(
         so_qc$nFeature_RNA >= nFeature_out &
         so_qc$percent.mt <= percent_mt_out
     )] <- "keep"
+  } else {
+    warning(
+      "No valid filtering method selected. All cells with nFeature_RNA > 200 retained"
+    )
+    so_qc$keep <- "keep"
   }
 
   return(so_qc)

SECURITY.md

@@ -2,7 +2,7 @@
 
 ## Maintained Versions
 
-Actively maintained versions of contained software will vary from repository to repository, or may not be relevant at all.  
+Actively maintained versions of contained software will vary from repository to repository, or may not be relevant at all.
 The developers of this repository will update this section if any actively maintained versions of the software need to be publicly disclosed. Otherwise, contact the developers directly for any version information.
 
 ## Vulnerability Disclosure:
@@ -16,4 +16,3 @@ Follow the instructions listed in the [HHS vulnerability disclosure policy](http
 1. Click on the **Security and quality** tab of this repository.
 2. Locate the **Report a vulnerability** button. If the button is not on the **Security and quality** landing page, look under the **Advisories** section in the side bar.
 3. Click the **Report a vulnerability** button and submit the form. The developers will receive a notification of your submission.
-

tests/testthat/test-filter_cells.R

@@ -4,14 +4,41 @@ test_that("filter_miQC", {
   expect_equal(length(which(pbmc_filt$keep == "keep")), 2140, tolerance = 5)
 })
 
+test_that("filter_miQC_case", {
+  set.seed(42)
+  pbmc_filt <- filter_cells(pbmc_processed, method = "mIqC")
+  expect_equal(length(which(pbmc_filt$keep == "keep")), 2140, tolerance = 5)
+})
+
 test_that("filter_manual", {
   set.seed(42)
   pbmc_filt <- filter_cells(pbmc_processed, method = "manual")
   expect_equal(length(which(pbmc_filt$keep == "keep")), 2510, tolerance = 5)
 })
 
+test_that("filter_manual_case", {
+  set.seed(42)
+  pbmc_filt <- filter_cells(pbmc_processed, method = "MAnUal")
+  expect_equal(length(which(pbmc_filt$keep == "keep")), 2510, tolerance = 5)
+})
+
 test_that("filter_mads", {
   set.seed(42)
   pbmc_filt <- filter_cells(pbmc_processed, method = "mads")
   expect_equal(length(which(pbmc_filt$keep == "keep")), 2590, tolerance = 5)
 })
+
+test_that("filter_mads_case", {
+  set.seed(42)
+  pbmc_filt <- filter_cells(pbmc_processed, method = "maDS")
+  expect_equal(length(which(pbmc_filt$keep == "keep")), 2590, tolerance = 5)
+})
+
+test_that("filter_nonexistent", {
+  set.seed(42)
+  expect_warning(
+    pbmc_filt <- filter_cells(pbmc_processed, method = "whatever"),
+    "No valid filtering"
+  )
+  expect_equal(ncol(pbmc_filt), 2638)
+})