From 7deb13423e5324a46ecbadc2ce863d016eb31113 Mon Sep 17 00:00:00 2001
From: "katharina.schmid" <katharina.schmid@helmholtz-muenchen.de>
Date: Fri, 25 Jun 2021 15:38:33 +0200
Subject: [PATCH] Added parameter cutoffVersion to function
 power.sameReadDepth.restrictedDoublets (missed when introducing the
 parameter)

---
 R/power.R                                     | 5 ++++-
 man/power.sameReadDepth.restrictedDoublets.Rd | 4 ++++
 2 files changed, 8 insertions(+), 1 deletion(-)

diff --git a/R/power.R b/R/power.R
index ad5b0c0..982f98f 100644
--- a/R/power.R
+++ b/R/power.R
@@ -658,7 +658,8 @@ power.sameReadDepth.withDoublets<-function(nSamples,nCells,ct.freq,
   } else if (multipletRateGrowth == "constant") {
     multipletFraction<-multipletRate
   } else {
-    stop("No known option for multipletRateGrowth. Use the values 'linear' or 'constant'.")
+    stop(paste("Input", multipletRateGrowth, "No known option for multipletRateGrowth.",
+               "Use the values 'linear' or 'constant'."))
   }
 
   #Check that the number of cells entered does not provide a multiplet rate of >100%
@@ -754,6 +755,7 @@ power.sameReadDepth.restrictedDoublets<-function(nSamples,nCells,ct.freq,
                               mappingEfficiency=0.8,
                               multipletRate=7.67e-06,multipletFactor=1.82,
                               min.UMI.counts=3,perc.indiv.expr=0.5,
+                              cutoffVersion="absolute",
                               nGenes=21000,samplingMethod="quantiles",
                               multipletRateGrowth="linear",
                               sign.threshold=0.05, MTmethod="Bonferroni",
@@ -779,6 +781,7 @@ power.sameReadDepth.restrictedDoublets<-function(nSamples,nCells,ct.freq,
                                           mappingEfficiency,
                                           multipletRate,multipletFactor,
                                           min.UMI.counts,perc.indiv.expr,
+                                          cutoffVersion,
                                           nGenes,samplingMethod,
                                           multipletRateGrowth,
                                           sign.threshold,
diff --git a/man/power.sameReadDepth.restrictedDoublets.Rd b/man/power.sameReadDepth.restrictedDoublets.Rd
index cbe899c..3ccd3a4 100644
--- a/man/power.sameReadDepth.restrictedDoublets.Rd
+++ b/man/power.sameReadDepth.restrictedDoublets.Rd
@@ -20,6 +20,7 @@ power.sameReadDepth.restrictedDoublets(
   multipletFactor = 1.82,
   min.UMI.counts = 3,
   perc.indiv.expr = 0.5,
+  cutoffVersion = "absolute",
   nGenes = 21000,
   samplingMethod = "quantiles",
   multipletRateGrowth = "linear",
@@ -72,6 +73,9 @@ of cells need to have a count value large than 0}
 individuals that need to have this gene expressed to define it as globally expressed;
 if number >=1 absolute number of individuals that need to have this gene expressed}
 
+\item{cutoffVersion}{Either "absolute" or "percentage" leading to different
+interpretations of min.counts (see description above)}
+
 \item{nGenes}{Number of genes to simulate (should match the number of genes used for the fitting)}
 
 \item{samplingMethod}{Approach to sample the gene mean values (either taking