From a47d8aa4c9ef611e24f8c450ff663464f052d335 Mon Sep 17 00:00:00 2001 From: Marijn Date: Thu, 26 Mar 2020 14:09:20 +0100 Subject: [PATCH] Updated Readme --- README.md | 42 +++++++++++++++++------------------------- 1 file changed, 17 insertions(+), 25 deletions(-) diff --git a/README.md b/README.md index 5af2eb3..fc1ce65 100644 --- a/README.md +++ b/README.md @@ -30,42 +30,39 @@ library(Matrix) library(Seurat) library(qlcMatrix) library(FastCAR) +``` +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 ``` - - - -``` -# This folder will contain the corrected cell matrix correctedMatrixFolder = c("Cellranger_output/sample1/corrected_feature_bc_matrix") - - +``` +Load both the cell matrix and the full matrix +``` cellMatrix = read.cell.matrix(cellExpressionFolder) fullMatrix = read.full.matrix(fullMatrixFolder) - ``` - -The following functions give an idea of the effect that different settings have on the ambient RNA profile. +The following functions give an idea of the effect that different settings have on the ambient RNA profile. +These are optional as they do take a few minutes and the default settings work fine Plotting the number of empty droplets, the number of genes identified in the ambient RNA, and the number of genes that will be corrected for at different UMI cutoffs, ``` -ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, start = 10, stop = 500, by = 10, contaminationChanceCutoff = 0.05) +ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, + start = 10, + stop = 500, + by = 10, + contaminationChanceCutoff = 0.05) + plot.ambient.profile(ambProfile) - ``` ![picture](Images/Example_profile.png) - Set the empty droplet cutoff and the contamination chance cutoff The empty droplet cutoff is the number of UMIs a droplet can contain at the most to be considered empty. @@ -79,17 +76,14 @@ In a cluster of a thousand cells divided into two groups there would be 2-3 cell Such low cell numbers are disregarded for differential expression analyses. ``` - emptyDropletCutoff = 100 contaminationChanceCutoff = 0.05 - ``` +Determine the ambient RNA profile and remove the ambient RNA from each cell ``` ambientProfile = determine.background.to.remove(fullMatrix, cellMatrix, emptyDropletCutoff, contaminationChanceCutoff) 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. @@ -100,14 +94,12 @@ write.corrected.matrix(cellMatrix, correctedMatrixFolder, ambientProfile) ``` -End with an example of getting some data out of the system or using it for a little demo -## Running the tests ## Authors -* **Marijn Berg** - *Initial work* +* **Marijn Berg** - m.berg@umcg.nl ## License