From c9eded2472ad4b6ebf9791efa41612537afa11b9 Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Mon, 24 Nov 2025 15:18:52 -0500
Subject: [PATCH 1/3] fix(transformTFIDF): return a sparse matrix instead of
 dense

---
 R/transformTFIDF.R | 5 +----
 1 file changed, 1 insertion(+), 4 deletions(-)

diff --git a/R/transformTFIDF.R b/R/transformTFIDF.R
index 394d0ba1..4f642da7 100644
--- a/R/transformTFIDF.R
+++ b/R/transformTFIDF.R
@@ -41,10 +41,7 @@ transformTFIDF <- function(mat, scale.factor = 1e5, binarize = FALSE) {
   tf <- t(t(mat.capped) / Matrix::colSums(mat.capped)) # compute term-frequency
   tf@x <- log1p(tf@x * scale.factor) # scale
   idf <- log(1 + ncol(mat.capped) / Matrix::rowSums(mat.capped)) # inverse-document frequency smooth
-  tfidf <- .tfidf(tf, idf) # transform
-
-  # cast back to a matrix since things like UMAP don't like sparse matrices
-  as.matrix(tfidf)
+  .tfidf(tf, idf) # transform
 }
 
 .binarize <- function(v) {

From 3ad20026ca944a0d26eac1bdb8be01cfa0cd7920 Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Mon, 3 Nov 2025 12:33:43 -0500
Subject: [PATCH 2/3] fix(shrinkBins): cbind assay and means to preserve
 sparsity

---
 R/shrinkBins.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/shrinkBins.R b/R/shrinkBins.R
index 136f4a67..9d392791 100644
--- a/R/shrinkBins.R
+++ b/R/shrinkBins.R
@@ -84,7 +84,7 @@ shrinkBins <- function(
 
   # bin the input
   bin.mat <- getBinMatrix(
-    mat = as.matrix(cbind(input.assay, prior.means)),
+    mat = cbind(input.assay, prior.means),
     genloc = rowRanges(x),
     chr = chr,
     res = res,

From c58ac5dec18cc10a5d81a1f636cce845923c0a56 Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Mon, 3 Nov 2025 12:33:27 -0500
Subject: [PATCH 3/3] chore(air): format style

---
 R/shrinkBins.R | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/R/shrinkBins.R b/R/shrinkBins.R
index 9d392791..8bf41c22 100644
--- a/R/shrinkBins.R
+++ b/R/shrinkBins.R
@@ -61,11 +61,12 @@ shrinkBins <- function(
   }
 
   # get the prior means
-  prior.means <- prior.means %||% getGlobalMeans(
-    obj = original.x,
-    targets = targets,
-    assay = assay
-  )
+  prior.means <- prior.means %||%
+    getGlobalMeans(
+      obj = original.x,
+      targets = targets,
+      assay = assay
+    )
 
   is.atac_or_rna <- assay %in% c("atac", "rna")
   input.fun <- if (jse) {