From 80b992390ecd9db2509e053de6211236f51e6344 Mon Sep 17 00:00:00 2001
From: LTLA <infinite.monkeys.with.keyboards@gmail.com>
Date: Sat, 14 Dec 2024 18:38:58 -0800
Subject: [PATCH] Added a separate check.missing.test= option that defaults to
 FALSE.

This avoids an unnecessary NA check for the test dataset, where it would be
very usual to have missing values. After all, the only purpose of this category
of arguments is to deal with NAs in the celldex references.
---
 R/SingleR.R    | 10 +++++++---
 man/SingleR.Rd |  8 +++++++-
 2 files changed, 14 insertions(+), 4 deletions(-)

diff --git a/R/SingleR.R b/R/SingleR.R
index a458fdb..2704c56 100644
--- a/R/SingleR.R
+++ b/R/SingleR.R
@@ -22,7 +22,9 @@
 #' if \code{test} is a \linkS4class{SummarizedExperiment} object.
 #' @param assay.type.ref An integer scalar or string specifying the assay of \code{ref} containing the relevant expression matrix,
 #' if \code{ref} is a \linkS4class{SummarizedExperiment} object (or is a list that contains one or more such objects).
-#' @param check.missing Logical scalar indicating whether rows should be checked for missing values (and if found, removed).
+#' @param check.missing.test Logical scalar indicating whether rows of \code{test} should be checked for missing values (and if found, removed).
+#' @param check.missing.ref Logical scalar indicating whether rows of \code{ref} should be checked for missing values (and if found, removed).
+#' @param check.missing Deprecated, use \code{check.missing.test} and \code{check.missing.ref} instead.
 #' @param num.threads Integer scalar specifying the number of threads to use for index building and classification.
 #' @param BNPARAM Deprecated and ignored.
 #' @param BPPARAM A \linkS4class{BiocParallelParam} object specifying how parallelization should be performed in other steps,
@@ -93,6 +95,8 @@ SingleR <- function(
     prune=TRUE, 
     assay.type.test = "logcounts", 
     assay.type.ref="logcounts", 
+    check.missing.test=FALSE, 
+    check.missing.ref=check.missing, 
     check.missing=TRUE, 
     num.threads = bpnworkers(BPPARAM),
     BNPARAM = NULL,
@@ -105,7 +109,7 @@ SingleR <- function(
 
     # We have to do all this row-subsetting at the start before trainSingleR,
     # otherwise 'test.genes' won't match up to the filtered 'test'.
-    test <- .to_clean_matrix(test, assay.type.test, check.missing, msg="test", BPPARAM=BPPARAM)
+    test <- .to_clean_matrix(test, assay.type.test, check.missing.test, msg="test", BPPARAM=BPPARAM)
 
     tmp.ref <- ref
     if (!is.list(tmp.ref) || is.data.frame(tmp.ref)) {
@@ -134,7 +138,7 @@ SingleR <- function(
         recompute=recompute,
         restrict = restrict, 
         test.genes=rownames(test),
-        check.missing=check.missing, 
+        check.missing=check.missing.ref, 
         BNPARAM=BNPARAM, 
         num.threads = num.threads, 
         BPPARAM=BPPARAM
diff --git a/man/SingleR.Rd b/man/SingleR.Rd
index ac07210..7262bc4 100644
--- a/man/SingleR.Rd
+++ b/man/SingleR.Rd
@@ -25,6 +25,8 @@ SingleR(
   prune = TRUE,
   assay.type.test = "logcounts",
   assay.type.ref = "logcounts",
+  check.missing.test = FALSE,
+  check.missing.ref = check.missing,
   check.missing = TRUE,
   num.threads = bpnworkers(BPPARAM),
   BNPARAM = NULL,
@@ -69,7 +71,11 @@ if \code{test} is a \linkS4class{SummarizedExperiment} object.}
 \item{assay.type.ref}{An integer scalar or string specifying the assay of \code{ref} containing the relevant expression matrix,
 if \code{ref} is a \linkS4class{SummarizedExperiment} object (or is a list that contains one or more such objects).}
 
-\item{check.missing}{Logical scalar indicating whether rows should be checked for missing values (and if found, removed).}
+\item{check.missing.test}{Logical scalar indicating whether rows of \code{test} should be checked for missing values (and if found, removed).}
+
+\item{check.missing.ref}{Logical scalar indicating whether rows of \code{ref} should be checked for missing values (and if found, removed).}
+
+\item{check.missing}{Deprecated, use \code{check.missing.test} and \code{check.missing.ref} instead.}
 
 \item{num.threads}{Integer scalar specifying the number of threads to use for index building and classification.}