4.1 Introductory text and philisophy of approach:

library(dplyr)
library(tidyr)
library(reshape2)
library(ReinforcementLearning)
options(stringsAsFactors = FALSE)
setwd("/Users/bowmanr/Projects/scDNA")
final_sample_summary<-readRDS(file="./data/final_sample_summary.rds")
pheno<-readRDS(file="./data/pheno.rds")

DTAI_genes <- c("ASXL1","DNMT3A","TET2","IDH1","IDH2")

DTAI_samples<-names(final_sample_summary)[do.call(c,lapply(names(final_sample_summary),function(sample){
  any(grepl(paste(DTAI_genes,sep="|",collapse="|"),colnames(final_sample_summary[[sample]]$NGT)))
}))]

DTAI_AML_samples <- pheno%>%
                        filter(Sample%in%DTAI_samples&grepl("AML",Dx))%>%
                        pull(Sample)