Commit 0f6cdfc7 authored by Sayed Rzgar Hosseini's avatar Sayed Rzgar Hosseini
Browse files

Upload New File

parent 1fe5a456
######################################################################################################################################################################################################### Expression Analysis:
#######################################################################################################################
### Fitnes genes :
Fitness<-read.csv("./Tables/Table15.csv")
FitnessGenes<-as.character(Fitness[,1])
FitnessValues<-Fitness[,2:326]
# Breast
Breast<-(c(19,44,70,84,85,87,88,89,91,102,122,169,171,172,173,174,179,225,323,32,86,92,170,307,175)-1)#Indices of Triple-Negative Breast cancer cell lines
Breast_Fitness<-FitnessValues[,Breast]
SEL<-which(apply(Breast_Fitness,1,sum)>0)
Breast_FitGenes<-FitnessGenes[SEL]
#Colorectal
LargeIntestine<-(c(28,38,39,40,41,52,80,90,94,95,109,126,157,159,160,161,162,163,176,258,262,290,291,292,293,302,303,304,305,308)-1)#Indices of Colorectal cancer cell lines
Colon_Fitness<-FitnessValues[,LargeIntestine]
SEL<-which(apply(Colon_Fitness,1,sum)>0)
Colon_FitGenes<-FitnessGenes[SEL]
######################################################################################################################################################################################################
## Excluding the Core-essential genes; Excluding the context essential genes, and Excluding the non-expressed genes
Candidate_Breast<-read.csv("./Tables/Table8.csv")$x
Candidate_Colorectal<-read.csv("./Tables/Table9.csv")$x
Breast_FitGenes<-intersect(Breast_FitGenes,Candidate_Breast)
Colon_FitGenes<-intersect(Colon_FitGenes,Candidate_Colorectal)
######################################################################################################################################################################################################breast_set5.2<-read.csv("/Users/rzgar/Desktop/Research/ENCORE_MEETING/BREAST1/Library_Prep/SET5.2.csv")
## Considering genes with Tractability II
Tractability_Breast<-read.csv("./Tables/Table16.csv")
Tractability_Colorectal<-read.csv("./Tables/Table17.csv")
Breast_FitGenes<-intersect(Tractability_Breast$Symbols[which(Tractability_Breast$Bucket==2)],Breast_FitGenes) #Breast fitness genes, Tractability group II
Colon_FitGenes<-intersect(Tractability_Colorectal$Symbols[which(Tractability_Colorectal$Bucket==2)],Colon_FitGenes) #Colorectal fitness genes, Tractability group II
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment