In the R script where you wish to use this algorithm... Load the contents of this algorithm, packages must be installed and are loaded:
- install.packages("Matrix")
- install.packages("proxy")
- install.packages("mclust")
- install.packages("vioplot")
- library(Matrix) ...
The seurat package is also required to be able to use functions in this code package:
require(Seurat)
Either set the working directory to the folder that contains your input file or incorporate it into:
input <- readRDS('exampleFolder\exampleInputFile.rds')
This input file should be preprocessed containing files, minimum:
- unspliced_cells_matrix
- spliced_cells_matrix
- ambient1_spliced
- ambient1_unspliced
- ambient2_spliced
- ambient2_unspliced
Inputs for Spliced_Processing and Unspliced_Processing needs an indication of which ambient files to use (1 or 2):
- Ambient file 1 contains all data including droplets with more RNA (>= 15 mRNA molecules detected) but not a valid cell - identified as ambient RNA
- Ambient file 2 contains all data including droplets with low RNA (< 15 mRNA molecules detected) - identified as ambient RNA