setwd("/Users/benayoun/Dropbox/Manuscripts_and_Publications/2018_aging_epigenomics_data_description/Aging_omics_paper/Github_folder/FigureS5_CIBERSORT/Immune_Gene_Expression/") # Ben Dulken
rm(list=ls())
library(ggplot2)
library(edgeR)
fpkm_glm_genefilt<-read.table("2016-02-05_ALL_global_variance estimate_DESeq2_LINEAR_model_with_age _log2_counts_matrix.txt",header=T,sep="\t")
#List of genes I profiled - various immune markers.
int_list<-c("Mertk","Cd34","Cd3eap","Cd47","Cd44","Cd8a","Cd4","Ccl5","Cd3e","Cd3g","Tcf7","Itgam","Ptprc","Klrb1c","Klrk1","Il2rb","Ccr3","Itga2b","Itga2","Kit","Itgb7","Fcgr1","Adgre1","Ly6c","Cd28")
# All cell types
fpkm_glm_int<-fpkm_glm_genefilt[na.omit(match(int_list,rownames(fpkm_glm_genefilt))),]
tissue<-c(rep("Liver",9),rep("Heart",9),rep("Cerebellum1",9),rep("OlfactoryBulb",8),rep("NPC",6))
age<-c(rep(c("3m","3m","3m","12m","12m","12m","29m","29m","29m"),3),"3m","3m","3m","12m","12m","29m","29m","29m","3m","3m","12m","12m","29m","29m")
# Remove NSPCs
fpkm_glm_int_noNPC<-fpkm_glm_genefilt[na.omit(match(int_list,rownames(fpkm_glm_genefilt))),-c(36:41)]
tissue_nonpc<-c(rep("Liver",9),rep("Heart",9),rep("Cerebellum1",9),rep("OlfactoryBulb",8))
age_nonpc<-c(rep(c("3m","3m","3m","12m","12m","12m","29m","29m","29m"),3),"3m","3m","3m","12m","12m","29m","29m","29m")
fpkm_glm_int
fpkm_glm_int_noNPC<-fpkm_glm_genefilt[na.omit(match(int_list,rownames(fpkm_glm_genefilt))),-c(36:41)]
tissue_nonpc<-c(rep("Liver",9),rep("Heart",9),rep("Cerebellum1",9),rep("OlfactoryBulb",8))
age_nonpc<-c(rep(c("3m","3m","3m","12m","12m","12m","29m","29m","29m"),3),"3m","3m","3m","12m","12m","29m","29m","29m")
my.heart <- fpkm_glm_int_noNPC[,tissue_nonpc == "Heart"]
my.liver <- fpkm_glm_int_noNPC[,tissue_nonpc == "Liver"]
my.cereb <- fpkm_glm_int_noNPC[,tissue_nonpc == "Cerebellum1"]
my.ob    <- fpkm_glm_int_noNPC[,tissue_nonpc == "OlfactoryBulb"]
my.heart
int_list<-c("Itgam","Ptprc")
fpkm_glm_int_noNPC<-fpkm_glm_genefilt[na.omit(match(int_list,rownames(fpkm_glm_genefilt))),-c(36:41)]
tissue_nonpc<-c(rep("Liver",9),rep("Heart",9),rep("Cerebellum1",9),rep("OlfactoryBulb",8))
age_nonpc<-c(rep(c("3m","3m","3m","12m","12m","12m","29m","29m","29m"),3),"3m","3m","3m","12m","12m","29m","29m","29m")
my.heart <- fpkm_glm_int_noNPC[,tissue_nonpc == "Heart"]
my.liver <- fpkm_glm_int_noNPC[,tissue_nonpc == "Liver"]
my.cereb <- fpkm_glm_int_noNPC[,tissue_nonpc == "Cerebellum1"]
my.ob    <- fpkm_glm_int_noNPC[,tissue_nonpc == "OlfactoryBulb"]
my.heart
wilcox.test(my.heart["Itgam",1:3],my.heart["Itgam",7:9], alternative = "less")
my.heart["Itgam",1:3]
wilcox.test(as.vector(my.heart["Itgam",1:3]),as.vector(my.heart["Itgam",7:9]), alternative = "less")
as.numeric(my.heart["Itgam",1:3])
wilcox.test(as.numeric(my.heart["Itgam",1:3]),as.vector(as.numeric["Itgam",7:9]), alternative = "less")
wilcox.test(as.numeric(my.heart["Itgam",1:3]),as.numeric(my.heart["Itgam",7:9]), alternative = "less")
wilcox.test(as.numeric(my.liver["Itgam",1:3]),as.numeric(my.liver["Itgam",7:9]), alternative = "less")
m
wilcox.test(as.numeric(my.cereb["Itgam",1:3]),as.numeric(my.cereb["Itgam",7:9]), alternative = "less")
wilcox.test(as.numeric(my.ob["Itgam",1:3]),as.numeric(my.ob["Itgam",7:9]), alternative = "less")
wilcox.test(as.numeric(my.ob["Itgam",1:3]),as.numeric(my.ob["Itgam",7:8]), alternative = "less")
wilcox.test(as.numeric(my.ob["Itgam",1:3]),as.numeric(my.ob["Itgam",6:8]), alternative = "less")
wilcox.test(as.numeric(my.heart["Ptprc",1:3]),as.numeric(my.heart["Ptprc",7:9]), alternative = "less")
wilcox.test(as.numeric(my.liver["Ptprc",1:3]),as.numeric(my.liver["Ptprc",7:9]), alternative = "less")
wilcox.test(as.numeric(my.cereb["Ptprc",1:3]),as.numeric(my.cereb["Ptprc",7:9]), alternative = "less")
wilcox.test(as.numeric(my.ob["Ptprc",1:3]),as.numeric(my.ob["Ptprc",6:8]), alternative = "less")
