105 lines
2.3 KiB
Markdown
105 lines
2.3 KiB
Markdown
# FastCAR
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FastCAR is an R package to remove ambient RNA from cells in droplet based single cell RNA sequencing data.
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## Getting Started
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These instructions will get you a copy of the project up and running on your local machine for development and testing purposes. See deployment for notes on how to deploy the project on a live system.
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### Prerequisites
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What things you need to install the software and how to install them
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```
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Give examples
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```
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### Installing
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FastCAR can be install from git with the following command.
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```
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devtools::install_git("https://git.web.rug.nl/P278949/FastCAR")
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```
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Running FastCAR is quite simple.
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First load the library and dependencies.
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```
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library(Matrix)
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library(Seurat)
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library(qlcMatrix)
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library(FastCAR)
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```
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```
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cellExpressionFolder = c("Cellranger_output/sample1/filtered_feature_bc_matrix/")
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fullMatrixFolder = c("Cellranger_output/sample1/raw_feature_bc_matrix/")
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```
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```
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# This folder will contain the corrected cell matrix
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correctedMatrixFolder = c("Cellranger_output/sample1/corrected_feature_bc_matrix")
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cellMatrix = read.cell.matrix(cellExpressionFolder)
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fullMatrix = read.full.matrix(fullMatrixFolder)
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```
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The following functions give an idea of the effect that different settings have on the ambient RNA profile
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```
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ambProfile = describe.ambient.RNA.sequence(fullCellMatrix = fullMatrix, start = 10, stop = 500, by = 10, contaminationChanceCutoff = 0.05)
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plot.ambient.profile(ambProfile)
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```
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![picture](https://git.web.rug.nl/P278949/FastCAR/src/branch/master/Images/Example_profile.png)
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Set
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```
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emptyDropletCutoff = 100
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contaminationChanceCutoff = 0.05
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```
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```
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ambientProfile = determine.background.to.remove(fullMatrix, cellMatrix, emptyDropletCutoff, contaminationChanceCutoff)
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cellMatrix = remove.background(cellMatrix, ambientProfile)
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```
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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.
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```
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write.corrected.matrix(cellMatrix, correctedMatrixFolder, ambientProfile)
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```
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End with an example of getting some data out of the system or using it for a little demo
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## Running the tests
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## Authors
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* **Marijn Berg** - *Initial work*
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## License
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This project is licensed under the GPL-3 License - see the [LICENSE.md](LICENSE.md) file for details
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