From 6e7fc48003fb54986d3ec26a102acc65ee2e305c Mon Sep 17 00:00:00 2001
From: Joshua Sodicoff <44811472+jsodicoff@users.noreply.github.com>
Date: Sun, 23 Jan 2022 21:39:04 -0500
Subject: [PATCH] Bug in getProportionMito

I noticed that getProportionMito gives an uninformative error (about indexing) if all mitochondrial genes found are not shared across all datasets. Using %in% instead of indexing ought to correct that.
---
 R/rliger.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/rliger.R b/R/rliger.R
index 81570570..465bf032 100755
--- a/R/rliger.R
+++ b/R/rliger.R
@@ -4587,7 +4587,7 @@ getProportionMito <- function(object, use.norm = FALSE) {
     data.use <- object@norm.data
   }
   percent_mito <- unlist(lapply(unname(data.use), function(x) {
-    colSums(x[mito.genes, ]) / colSums(x)
+    colSums(x[rownames(x) %in% mito.genes, ]) / colSums(x)
   }), use.names = TRUE)
   
   return(percent_mito)
@@ -7161,4 +7161,4 @@ calcNormLoadings = function(object) {
   }
   
   return(results)
-}
\ No newline at end of file
+}