Protein Imputation

# Imputation script from: https://github.com/WangLab-MSSM/DreamAI
require("cluster")
require("survival")
require("randomForest")
require("missForest")
require("glmnet")
require("Rcpp")
require("foreach")
require("itertools")
require("iterators")
require("Matrix")
require("devtools")
# Needed to install impute as well
#BiocManager::install("impute") #, version = "3.8")
require("impute")
require("remotes")
# You need to install via the below link
#install_github("WangLab-MSSM/DreamAI/Code")

library("DreamAI")
prot_data <- read.csv('../data/raw_downloads/CPTAC/6_CPTAC3_CCRCC_Whole_abundance_gene_protNorm=2_CB.tsv', sep='\t')
colnames(prot_data)
prot_num_data <- prot_data[, 5:length(colnames(prot_data))]
rownames(prot_num_data) <- prot_data$Index
imputed_data <- DreamAI(prot_num_data, k = 10, maxiter_MF = 10, ntree = 100,
                        maxnodes = NULL, maxiter_ADMIN = 30, tol = 10^(-2),
                        gamma_ADMIN = NA, gamma = 50, CV = FALSE,
                        fillmethod = "row_mean", maxiter_RegImpute = 10,
                        conv_nrmse = 1e-06, iter_SpectroFM = 40, method = c("KNN",
                                                                            "MissForest", "ADMIN", "Birnn", "SpectroFM", "RegImpute"),
                        out = c("Ensemble"))

ens_data <- imputed_data$Ensemble
write.csv(ens_data, '../data/sircle/F1_DE_input_TvN/6_CPTAC3_CCRCC_Whole_abundance_gene_protNorm=2_CB_DreamAI-imputed.csv')