From 1663262d07d62c4803307eeeb4e970cf836ff63e Mon Sep 17 00:00:00 2001
From: Jonathan Griffiths <7976085+jonathangriffiths@users.noreply.github.com>
Date: Tue, 23 Jul 2024 14:19:51 +0100
Subject: [PATCH] deprecate beachmat::whichNonZero (#111)

* deprecate beachmat::whichNonZero
---
 DESCRIPTION    |  4 ++--
 NAMESPACE      |  3 ++-
 R/emptyDrops.R | 17 ++++++++---------
 3 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index fe9144d..f5b61d7 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: DropletUtils
-Version: 1.25.1
-Date: 2024-07-09
+Version: 1.25.2
+Date: 2024-07-23
 Title: Utilities for Handling Single-Cell Droplet Data
 Authors@R: c(
     person("Aaron", "Lun", role = "aut"),
diff --git a/NAMESPACE b/NAMESPACE
index fdd3dfe..ef24259 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -86,10 +86,11 @@ importFrom(S4Vectors,extractROWS)
 importFrom(S4Vectors,make_zero_col_DFrame)
 importFrom(S4Vectors,metadata)
 importFrom(SingleCellExperiment,SingleCellExperiment)
+importFrom(SparseArray,nzvals)
+importFrom(SparseArray,nzwhich)
 importFrom(SummarizedExperiment,assay)
 importFrom(SummarizedExperiment,colData)
 importFrom(beachmat,colBlockApply)
-importFrom(beachmat,whichNonZero)
 importFrom(dqrng,generateSeedVectors)
 importFrom(edgeR,goodTuringProportions)
 importFrom(edgeR,q2qnbinom)
diff --git a/R/emptyDrops.R b/R/emptyDrops.R
index 1b8479a..65cedee 100644
--- a/R/emptyDrops.R
+++ b/R/emptyDrops.R
@@ -311,16 +311,16 @@ testEmptyDrops <- function(m, lower=100, niters=10000, test.ambient=FALSE, ignor
     list(seeds=seeds.per.core, streams=streams.per.core)
 }
 
-#' @importFrom beachmat whichNonZero
+#' @importFrom SparseArray nzwhich nzvals
 .compute_multinom_prob_data <- function(block, prop, alpha=Inf, BPPARAM=SerialParam())
 # Efficiently calculates the data-dependent component of the log-multinomial probability
 # for a column-wise chunk of the full matrix (or, indeed, the full matrix itself).
 # Also does so for the Dirichlet-multinomial log-probability for a given 'alpha'.
 {
-    nonzero <- whichNonZero(block)
-    i <- nonzero$i
-    j <- nonzero$j
-    x <- nonzero$x
+    idx <- nzwhich(block, arr.ind=TRUE)
+    i <- idx[,1]
+    j <- idx[,2]
+    x <- nzvals(block)
 
     if (is.infinite(alpha)) {
         p.n0 <- x * log(prop[i]) - lfactorial(x)
@@ -346,14 +346,13 @@ testEmptyDrops <- function(m, lower=100, niters=10000, test.ambient=FALSE, ignor
     }
 }
 
-#' @importFrom beachmat whichNonZero
+#' @importFrom SparseArray nzwhich nzvals
 #' @importFrom stats optimize 
 .estimate_alpha <- function(mat, prop, totals, interval=c(0.01, 10000))
 # Efficiently finds the MLE for the overdispersion parameter of a Dirichlet-multinomial distribution.
 {
-    nonzero <- whichNonZero(mat)
-    i <- nonzero$i
-    x <- nonzero$x
+    i <- nzwhich(mat, arr.ind=TRUE)[,1]
+    x <- nzvals(mat)
 
     per.prop <- prop[i] 
     LOGLIK <- function(alpha) {