R/main.R

In carmonalab/TILPRED: Tumor-infiltrating CD8+ T-cell state predictor for scRNA-seq data

#install.packages("BiocManager")
#install.packages("doParallel")
#install.packages("doRNG")
#BiocManager::install("GenomeInfoDbData",type="source")
#BiocManager::install("AUCell")
#BiocManager::install("SingleCellExperiment",type="source")
#library(AUCell)
#library(SingleCellExperiment)
#library(doParallel)
#library(doRNG)


glm_coefs <- readRDS("data/coefs.list.rds")
sigs <- readRDS("data/cellTypeSignatures_mouse.Rds")
cellTypeHumanSigs <- readRDS("data/cellTypeSignatures_human.Rds")
orthologMap <- readRDS("data/mapHsa_vs_Mmu_Orthologs.rds")



predictorSigs=unique(unlist(lapply(glm_coefs,names)))
classNames=names(glm_coefs)