Single Cell Imputation

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scImpute

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scimpute(# full path to raw count matrix                                                                     
    count_path = '/home/ubuntu/download/cart/AHCA.nonimmu.trachea.csv',                                   
    infile = "csv",           # format of input file                                                      
    outfile = "csv",          # format of output file                                                     
    out_dir = "/home/ubuntu/download/cart/AHCA.nonimmu.trachea.scimpute_dropprob0.3", # full path to output directory                                                                                           
    labeled = FALSE,          # cell type labels not available                                            
    drop_thre = 0.3,          # threshold set on dropout probability                                      
    Kcluster = 2,             # 2 cell subpopulations                                                     
    ncores = 24)              # number of cores used in parallel computation

DrImpute

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X = read.csv('/home/ubuntu/download/cart/AHCA.nonimmu.trachea.csv')
dim(X)
X.log <- log(X + 1)
X.log <- as.matrix(X.log)  
set.seed(1)
X.imp <- DrImpute(X.log, mc.cores=20) 
X.imp.count = exp(X.imp) - 1 
write.csv(X.imp.count,'/home/ubuntu/download/cart/AHCA.trachea.drimpute.csv')