From 40765c3a42c029f0285e1860f83c17988bbc1545 Mon Sep 17 00:00:00 2001
From: Marijn <mbergwork@gmail.com>
Date: Mon, 27 Apr 2020 15:50:48 +0200
Subject: [PATCH] updated readme and made the new function match the rest of
 the formatting

---
 R/FastCAR_Base.R |  2 +-
 README.md        | 25 ++++++++++++++++---------
 2 files changed, 17 insertions(+), 10 deletions(-)

diff --git a/R/FastCAR_Base.R b/R/FastCAR_Base.R
index c380cb3..cc50f34 100644
--- a/R/FastCAR_Base.R
+++ b/R/FastCAR_Base.R
@@ -146,7 +146,7 @@ plot.ambient.profile = function(ambientProfile){
 
 # I noticed that the number of genes removed tends to even out over time
 # Test whether the point where this first happens is a good empty cutoff point
-recommendedRemoval = function(ambientProfile){
+recommend.empty.cutoff = function(ambientProfile){
   highestNumberOfGenes = max(ambientProfile[,3])
   firstOccurence = match(highestNumberOfGenes, ambientProfile[,3])
   return(as.numeric(rownames(ambientProfile[firstOccurence,])))
diff --git a/README.md b/README.md
index 3d80de1..12b8bc6 100644
--- a/README.md
+++ b/README.md
@@ -26,11 +26,6 @@ Specify the locations of the expression matrices
 cellExpressionFolder  = c("Cellranger_output/sample1/filtered_feature_bc_matrix/")
 fullMatrixFolder      = c("Cellranger_output/sample1/raw_feature_bc_matrix/")
 ```
-Set a location for storing the corrected cell/gene matrix
-
-```
-correctedMatrixFolder = c("Cellranger_output/sample1/corrected_feature_bc_matrix")
-```
 Load both the cell matrix and the full matrix
 ```
 cellMatrix     = read.cell.matrix(cellExpressionFolder)
@@ -64,6 +59,15 @@ As we developed FastCAR specifically for differential expression analyses betwee
 In a cluster of a thousand cells divided into two groups there would be 2-3 cells per group with ambient RNA contamination of any given gene.
 Such low cell numbers are disregarded for differential expression analyses.
 
+There is an experimental function that gives a recommendation based on the ambient profiling results.
+This selects the first instance of the maximum number of genes being corrected for.
+I have no idea yet if this is actually a good idea.
+
+```
+emptyDropletCutoff = recommend.empty.cutoff(ambProfile)
+```
+
+
 ```
 emptyDropletCutoff        = 100 
 contaminationChanceCutoff = 0.05
@@ -75,12 +79,10 @@ ambientProfile = determine.background.to.remove(fullMatrix, cellMatrix, emptyDro
 cellMatrix     = remove.background(cellMatrix, ambientProfile)
 ```
 
-Finally write the corrected cell/gene matrix to a file, this matrix can be used in Seurat the same way as any other cell/gene matrix.
+This corrected matrix can be used to to make a Seurat object
 
 ```
-
-write.corrected.matrix(cellMatrix, correctedMatrixFolder, ambientProfile)
-
+seuratObject = CreateSeuratObject(cellMatrix) 
 ```
 
 
@@ -96,3 +98,8 @@ This project is licensed under the GPL-3 License - see the [LICENSE.md](LICENSE.
 
 ### v0.1
 First fully working version of the R package
+
+### v0.2
+Fixed function to write the corrected matrix to file.
+Added readout of which genes will be corrected for and how many reads will be removed per cell
+Added some input checks to functions