From 3d05ca7244521e1e908123a9faec03ff5b1feb6b Mon Sep 17 00:00:00 2001
From: Will Nickols <willnickols@college.harvard.edu>
Date: Thu, 1 Aug 2024 16:32:52 -0400
Subject: [PATCH] Update utility_scripts.R

---
 R/utility_scripts.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/utility_scripts.R b/R/utility_scripts.R
index 74c5fa9..628fc9c 100644
--- a/R/utility_scripts.R
+++ b/R/utility_scripts.R
@@ -79,6 +79,7 @@ CLRnorm = function(features, zero_threshold) {
 # From metagenomeSeq #
 ######################
 
+# The zero threshold isn't correct here yet, but we're probably removing these
 calcNormFactors <- function(x, p = cumNormStat(x)) {
   xx <- x
   xx[xx == 0] <- NA
@@ -182,6 +183,7 @@ CSSnorm = function(features, zero_threshold) {
 # From edgeR #
 ##############
 
+# The zero threshold isn't correct here yet, but we're probably removing these
 .calcFactorQuantile <- function (data, lib.size, p=0.75)
   #	Generalized version of upper-quartile normalization
   #	Mark Robinson and Gordon Smyth