my.NPCs.dwn <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K4me3_height/OB_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K4me3_height/OB_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "DOWN"
my.cereb.up$Direction  <- "UP"
my.heart.dwn$Direction <- "DOWN"
my.heart.up$Direction  <- "UP"
my.liver.dwn$Direction <- "DOWN"
my.liver.up$Direction  <- "UP"
my.NPCs.dwn$Direction  <- "DOWN"
my.NPCs.up$Direction   <- "UP"
my.ob.dwn$Direction    <- "DOWN"
my.ob.up $Direction    <- "UP"
# get only FDR < 0.05
get_sigs <- function (homer.data) {
my.sigs <- homer.data$q.value..Benjamini. < 0.05
return(homer.data[my.sigs,])
}
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
# read results tables
my.cereb.dwn <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.cereb.up <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.heart.dwn <- read.csv('H3K4me3_height/Heart_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.heart.up <- read.csv('H3K4me3_height/Heart_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.liver.dwn <- read.csv('H3K4me3_height/Liver_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.liver.up <- read.csv('H3K4me3_height/Liver_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.NPCs.dwn <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K4me3_height/OB_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K4me3_height/OB_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
get_sigs <- function (homer.data) {
my.sigs <- homer.data$q.value..Benjamini. < 0.05
return(homer.data[my.sigs,])
}
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
my.breadth.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )
my.cereb.dwn
my.cereb.up
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )
my.ob.up
# read results tables
my.cereb.dwn <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.cereb.up <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.heart.dwn <- read.csv('H3K4me3_height/Heart_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.heart.up <- read.csv('H3K4me3_height/Heart_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.liver.dwn <- read.csv('H3K4me3_height/Liver_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.liver.up <- read.csv('H3K4me3_height/Liver_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.NPCs.dwn <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K4me3_height/OB_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K4me3_height/OB_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )
my.cereb.dwn
colnames(my.cereb.dwn)
# get only FDR < 0.05
get_sigs <- function (homer.data) {
my.sigs <- homer.data$q.value..Benjamini. < 0.05
colnames(homer.data) <- c("Motif.Name","Consensus","P.value",
"Log.P.value","q.value","Number.Target.Sequences.with.Motif",
"Percent.Target.Sequences.with.Motif","Number.Background.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,
"Tissue","Direction")
return(homer.data[my.sigs,])
}
###############################################################
#################### H3K4me3 intensity ########################
# read results tables
my.cereb.dwn <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.cereb.up <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.heart.dwn <- read.csv('H3K4me3_height/Heart_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.heart.up <- read.csv('H3K4me3_height/Heart_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.liver.dwn <- read.csv('H3K4me3_height/Liver_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.liver.up <- read.csv('H3K4me3_height/Liver_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.NPCs.dwn <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K4me3_height/OB_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K4me3_height/OB_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )
my.intensity.motifs
setwd('/Volumes/BB_Backup_3//BD_aging_project/ChIP-seq/All_tissues_analysis/Motif_analyses/HOMER/Known_results_tables/')
options(stringsAsFactors = FALSE);
# 2017-08-30
# process top KNOWN enrichments for aging omics paper
# get only FDR < 0.05
get_sigs <- function (homer.data, my.fdr= 0.1) {
my.sigs <- homer.data$q.value..Benjamini. < my.fdr
colnames(homer.data) <- c("Motif.Name","Consensus","P.value",
"Log.P.value","q.value","Number.Target.Sequences.with.Motif",
"Percent.Target.Sequences.with.Motif","Number.Background.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,
"Tissue","Direction")
return(homer.data[my.sigs,])
}
###############################################################
#################### H3K4me3 intensity ########################
# read results tables
my.cereb.dwn <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.cereb.up <- read.csv('H3K4me3_height/Cerebellum_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.heart.dwn <- read.csv('H3K4me3_height/Heart_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.heart.up <- read.csv('H3K4me3_height/Heart_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.liver.dwn <- read.csv('H3K4me3_height/Liver_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.liver.up <- read.csv('H3K4me3_height/Liver_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.NPCs.dwn <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K4me3_height/NPCs_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K4me3_height/OB_H3K4me3_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K4me3_height/OB_H3K4me3_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )
my.intensity.motifs
my.colnames <- c("Motif.Name","Consensus","P.value",
"Log.P.value","q.value","Number.Target.Sequences.with.Motif",
"Percent.Target.Sequences.with.Motif","Number.Background.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,
"Tissue","Direction")
my.selected.colnames <- c("Motif.Name","Consensus","P.value","q.value","Percent.Target.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,         "Tissue","Direction")
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )[,my.selected.colnames]
my.intensity.motifs
View(my.intensity.motifs)
write.table(my.intensity.motifs, file = paste(Sys.Date(),"H3K4me3_intensity_changes_with_age_Homer_known_Enriched_motifs.FDR0.1.txt", sep ="_"),
quote = F, row.names = F, sep = "\t")
# read results tables
my.cereb.dwn <- read.csv("H3K4me3_breadth/Cerebellum_GAINED_H3K4me3_breadth_knownResults.txt"  ,header =T, sep ="\t")
my.cereb.up  <- read.csv("H3K4me3_breadth/Cerebellum_LOST_H3K4me3_breadth_knownResults.txt"    ,header =T, sep ="\t")
my.heart.dwn <- read.csv("H3K4me3_breadth/Heart_GAINED_H3K4me3_breadth_knownResults.txt"       ,header =T, sep ="\t")
my.heart.up  <- read.csv("H3K4me3_breadth/Heart_LOST_H3K4me3_breadth_knownResults.txt"         ,header =T, sep ="\t")
my.liver.dwn <- read.csv("H3K4me3_breadth/Liver_GAINED_H3K4me3_breadth_knownResults.txt"       ,header =T, sep ="\t")
my.liver.up  <- read.csv("H3K4me3_breadth/Liver_LOST_H3K4me3_breadth_knownResults.txt"         ,header =T, sep ="\t")
my.NPCs.dwn  <- read.csv("H3K4me3_breadth/NPCs_GAINED_H3K4me3_breadth_knownResults.txt"        ,header =T, sep ="\t")
my.NPCs.up   <- read.csv("H3K4me3_breadth/NPCs_LOST_H3K4me3_breadth_knownResults.txt"          ,header =T, sep ="\t")
my.ob.dwn    <- read.csv("H3K4me3_breadth/OB_GAINED_H3K4me3_breadth_knownResults.txt"          ,header =T, sep ="\t")
my.ob.up     <- read.csv("H3K4me3_breadth/OB_LOST_H3K4me3_breadth_knownResults.txt"            ,header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )[,my.selected.colnames]
my.intensity.motifs
write.table(my.intensity.motifs, file = paste(Sys.Date(),"H3K4me3_breadth_changes_with_age_Homer_known_Enriched_motifs.FDR0.1.txt", sep ="_"),
quote = F, row.names = F, sep = "\t")
###################################################################################################
###################################### H3K27ac intensity ##########################################
###################################################################################################
# read results tables
my.cereb.dwn <- read.csv('H3K27ac_height/Cerebellum_H3K27ac_height_decreased_knownResults.txt',header =T, sep ="\t")
my.cereb.up <- read.csv('H3K27ac_height/Cerebellum_H3K27ac_height_increased_knownResults.txt',header =T, sep ="\t")
my.heart.dwn <- read.csv('H3K27ac_height/Heart_H3K27ac_height_decreased_knownResults.txt',header =T, sep ="\t")
my.heart.up <- read.csv('H3K27ac_height/Heart_H3K27ac_height_increased_knownResults.txt',header =T, sep ="\t")
my.liver.dwn <- read.csv('H3K27ac_height/Liver_H3K27ac_height_decreased_knownResults.txt',header =T, sep ="\t")
my.liver.up <- read.csv('H3K27ac_height/Liver_H3K27ac_height_increased_knownResults.txt',header =T, sep ="\t")
my.NPCs.dwn <- read.csv('H3K27ac_height/NPCs_H3K27ac_height_decreased_knownResults.txt',header =T, sep ="\t")
my.NPCs.up <- read.csv('H3K27ac_height/NPCs_H3K27ac_height_increased_knownResults.txt',header =T, sep ="\t")
my.ob.dwn <- read.csv('H3K27ac_height/OB_H3K27ac_height_decreased_knownResults.txt',header =T, sep ="\t")
my.ob.up <- read.csv('H3K27ac_height/OB_H3K27ac_height_increased_knownResults.txt',header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.NPCs.dwn$Tissue  <- "NPCs"
my.NPCs.up$Tissue   <- "NPCs"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.ob.up $Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.NPCs.dwn$Direction  <- "Decreased"
my.NPCs.up$Direction   <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
my.ob.up $Direction    <- "Increased"
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.NPCs.dwn  <- get_sigs(my.NPCs.dwn )
my.NPCs.up   <- get_sigs(my.NPCs.up  )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.ob.up     <- get_sigs(my.ob.up    )
my.intensity.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.NPCs.dwn ,
my.NPCs.up  ,
my.ob.dwn   ,
my.ob.up    )[,my.selected.colnames]
write.table(my.intensity.motifs, file = paste(Sys.Date(),"H3K27ac_intensity_changes_with_age_Homer_known_Enriched_motifs.FDR0.1.txt", sep ="_"),
quote = F, row.names = F, sep = "\t")
setwd('/Volumes/BB_Backup_3//BD_aging_project/ChIP-seq/All_tissues_analysis/Motif_analyses/HOMER/Known_results_tables/')
options(stringsAsFactors = FALSE);
# 2017-08-30
# process top KNOWN enrichments for aging omics paper
# get only FDR < 0.05
get_sigs <- function (homer.data, my.fdr= 0.1) {
my.sigs <- homer.data$q.value..Benjamini. < my.fdr
colnames(homer.data) <- c("Motif.Name","Consensus","P.value",
"Log.P.value","q.value","Number.Target.Sequences.with.Motif",
"Percent.Target.Sequences.with.Motif","Number.Background.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,
"Tissue","Direction")
return(homer.data[my.sigs,])
}
my.selected.colnames <- c("Motif.Name","Consensus","P.value","q.value","Percent.Target.Sequences.with.Motif","Percent.Background.Sequences.with.Motif" ,         "Tissue","Direction")
###################################################################################################
###################################### H3K27ac SE ##########################################
###################################################################################################
# read results tables
my.cereb.dwn <- read.csv("H3K27ac_SE/Cerebellum_H3K27ac_height_SELite_decreased_knownResults.txt"   ,header =T, sep ="\t")
my.cereb.up  <- read.csv("H3K27ac_SE/Cerebellum_H3K27ac_height_SELite_increased_knownResults.txt"   ,header =T, sep ="\t")
my.heart.dwn <- read.csv("H3K27ac_SE/Heart_H3K27ac_height_SELite_decreased_knownResults.txt"        ,header =T, sep ="\t")
my.heart.up  <- read.csv("H3K27ac_SE/Heart_H3K27ac_height_SELite_increased_knownResults.txt"        ,header =T, sep ="\t")
my.liver.dwn <- read.csv("H3K27ac_SE/Liver_H3K27ac_height_SELite_decreased_knownResults.txt"        ,header =T, sep ="\t")
my.liver.up  <- read.csv("H3K27ac_SE/Liver_H3K27ac_height_SELite_increased_knownResults.txt"        ,header =T, sep ="\t")
my.ob.dwn    <- read.csv("H3K27ac_SE/OB_H3K27ac_height_SELite_decreased_knownResults.txt"           ,header =T, sep ="\t")
# add necessary data
my.cereb.dwn$Tissue <- "Cerebellum"
my.cereb.up$Tissue  <- "Cerebellum"
my.heart.dwn$Tissue <- "Heart"
my.heart.up$Tissue  <- "Heart"
my.liver.dwn$Tissue <- "Liver"
my.liver.up$Tissue  <- "Liver"
my.ob.dwn$Tissue    <- "OlfactoryBulb"
my.cereb.dwn$Direction <- "Decreased"
my.cereb.up$Direction  <- "Increased"
my.heart.dwn$Direction <- "Decreased"
my.heart.up$Direction  <- "Increased"
my.liver.dwn$Direction <- "Decreased"
my.liver.up$Direction  <- "Increased"
my.ob.dwn$Direction    <- "Decreased"
# apply function
my.cereb.dwn <- get_sigs(my.cereb.dwn)
my.cereb.up  <- get_sigs(my.cereb.up )
my.heart.dwn <- get_sigs(my.heart.dwn)
my.heart.up  <- get_sigs(my.heart.up )
my.liver.dwn <- get_sigs(my.liver.dwn)
my.liver.up  <- get_sigs(my.liver.up )
my.ob.dwn    <- get_sigs(my.ob.dwn   )
my.SE.motifs <- rbind(my.cereb.dwn,
my.cereb.up ,
my.heart.dwn,
my.heart.up ,
my.liver.dwn,
my.liver.up ,
my.ob.dwn   )[,my.selected.colnames]
write.table(my.SE.motifs, file = paste(Sys.Date(),"H3K27ac_SE_changes_with_age_Homer_known_Enriched_motifs.FDR0.1.txt", sep ="_"),
quote = F, row.names = F, sep = "\t")
###################################################################################################
###################################################################################################
###################################################################################################
#setwd('/Volumes/MyBook_3/BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/Summary')
setwd('/Volumes/BB_Backup_3//BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/Summary')
options(stringsAsFactors=F)
#setwd('/Volumes/MyBook_3/BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/')
setwd('/Volumes/BB_Backup_3//BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/')
library('mHG')
options(stringsAsFactors=F)
source('GOrilla_statistics_functions.R')
install.packages('mHG')
library('mHG')
#setwd('/Volumes/MyBook_3/BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/')
setwd('/Volumes/BB_Backup_3//BD_aging_project/RNAseq/All_tissues_analysis/CIBERSORT/InSIlico_Immune_removal/Pathway_enrichment/')
library('mHG')
options(stringsAsFactors=F)
source('GOrilla_statistics_functions.R')
my.gmt.sets <-paste("/Volumes/BB_Backup_3//BD_aging_project/Pathway_Enrichment/Param/", list.files("/Volumes/MyBook_3/BD_aging_project/Pathway_Enrichment/Param",pattern = "\\.gmt$"), sep="/")
my.gmt.set.names <- c("KEGG_2017_no_diseases_UC","KEGG_2017_no_diseases","KEGG_2017_All")
cbind(my.gmt.sets, my.gmt.set.names)
list.files("/Volumes/MyBook_3/BD_aging_project/Pathway_Enrichment/Param"
,pattern = "\\.gmt$")
setwd('/Volumes/BB_Backup_3//BD_aging_project/Venn_different_molecules')
options(stringsAsFactors=F)
library('Vennerable')
R install command: install.packages("Vennerable", repos="http://R-Forge.R-project.org")
install.packages("Vennerable", repos="http://R-Forge.R-project.org")
install.packages(''reshape'')
install.packages('reshape')
install.packages(''reshape'')
install.packages("Vennerable", repos="http://R-Forge.R-project.org")
library('Vennerable')
