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06d-GO_analysis.R
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06d-GO_analysis.R
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setwd("readcounts_braker_gtf/")
library(topGO)
#Do GO analysis
ParthSex = read.table("Parthenogenic_vs_Sexual_DESeq_all.txt",header=T)
PartiSex = read.table("Partial_vs_Sexual_DESeq_all.txt",header=T)
ParthParti = read.table("Parthenogenic_vs_Partial_DESeq_all.txt",header=T)
all.tab = read.table("AllContrastsMerged_DESeq_allGenes.txt",header=T)
#Subset to sginificant genes
ParthSex.sign = all.tab[all.tab$padj.ParthSex < 0.05,]
ParthParti.sign = all.tab[all.tab$padj.ParthParti < 0.05,]
PartiSex.sign = all.tab[all.tab$padj.PartiSex < 0.05,]
#Remove not annotated genes
all.tab.naEx = all.tab[!is.na(all.tab$primary_FBgn),]
nrow(all.tab.naEx)
#Further split up into up and down regulates
ParthSex.naEx.up = all.tab.naEx[all.tab.naEx$log2FoldChange.ParthSex > 0,]
ParthSex.naEx.down = all.tab.naEx[all.tab.naEx$log2FoldChange.ParthSex < 0,]
PartiSex.naEx.up = all.tab.naEx[all.tab.naEx$log2FoldChange.PartiSex > 0,]
PartiSex.naEx.down = all.tab.naEx[all.tab.naEx$log2FoldChange.PartiSex < 0,]
ParthParti.naEx.up = all.tab.naEx[all.tab.naEx$log2FoldChange.ParthParti > 0,]
ParthParti.naEx.down = all.tab.naEx[all.tab.naEx$log2FoldChange.ParthParti < 0,]
####################################################################################
#Define cutoff for significance
geneSelFunc = function (score) {
return(score < 0.05)
}
# Some genes have multiple annotations to D. melanogaster - decided to randomly select one
###############################################################
#ALL SIGNIFICANT GENES (up/down regulated not separated)
###############################################################
rounds = 100
fdr.cutoff = 0.1
algorithm = "classic"
ParthSex.sign.terms.Fish = NULL
ParthSex.sign.terms.KS = NULL
PartiSex.sign.terms.Fish = NULL
PartiSex.sign.terms.KS = NULL
ParthParti.sign.terms.Fish = NULL
ParthParti.sign.terms.KS = NULL
for (i in 1:rounds){
print(i)
fbgn.list = strsplit(as.character(all.tab.naEx$primary_FBgn),";")
fbgn.list.random = lapply(fbgn.list, function(x) sample(x,1))
#Create vactors with padj
ParthSex.vect = c(all.tab.naEx$padj.ParthSex)
PartiSex.vect = c(all.tab.naEx$padj.PartiSex)
ParthParti.vect = c(all.tab.naEx$padj.ParthParti)
names(ParthSex.vect) = unlist(fbgn.list.random)
names(PartiSex.vect) = unlist(fbgn.list.random)
names(ParthParti.vect) = unlist(fbgn.list.random)
#Summarize by taking median
ParthSex.vect = tapply(ParthSex.vect,names(ParthSex.vect),median)
PartiSex.vect = tapply(PartiSex.vect,names(PartiSex.vect),median)
ParthParti.vect = tapply(ParthParti.vect,names(ParthParti.vect),median)
#do GO analysis
ParthSex.GO = top_go_analysis(ParthSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
PartiSex.GO = top_go_analysis(PartiSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
ParthParti.GO = top_go_analysis(ParthParti.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
#add round numbering
ParthSex.GO = lapply(ParthSex.GO, function(x) cbind(x,Round = i, No_of_Genes = length(ParthSex.vect), No_candidates = length(ParthSex.vect[ParthSex.vect<0.05]) ))
PartiSex.GO = lapply(PartiSex.GO, function(x) cbind(x,Round = i, No_of_Genes = length(PartiSex.vect), No_candidates = length(PartiSex.vect[PartiSex.vect<0.05])))
ParthParti.GO = lapply(ParthParti.GO, function(x) cbind(x,Round = i, No_of_Genes = length(ParthParti.vect), No_candidates = length(ParthParti.vect[ParthParti.vect<0.05])))
#Select significant categories
ParthSex.GO.signFisher = ParthSex.GO$P_Fisher[ParthSex.GO$P_Fisher$FDR < fdr.cutoff,]
ParthSex.GO.signKS = ParthSex.GO$P_KS[ParthSex.GO$P_KS$FDR < fdr.cutoff,]
PartiSex.GO.signFisher = PartiSex.GO$P_Fisher[PartiSex.GO$P_Fisher$FDR < fdr.cutoff,]
PartiSex.GO.signKS = PartiSex.GO$P_KS[PartiSex.GO$P_KS$FDR < fdr.cutoff,]
ParthParti.GO.signFisher = ParthParti.GO$P_Fisher[ParthParti.GO$P_Fisher$FDR < fdr.cutoff,]
ParthParti.GO.signKS = ParthParti.GO$P_KS[ParthParti.GO$P_KS$FDR < fdr.cutoff,]
#Make vector with significant categories
ParthSex.sign.terms.Fish = rbind(ParthSex.sign.terms.Fish, ParthSex.GO.signFisher)
ParthSex.sign.terms.KS = rbind(ParthSex.sign.terms.KS, ParthSex.GO.signKS)
PartiSex.sign.terms.Fish = rbind(PartiSex.sign.terms.Fish, PartiSex.GO.signFisher)
PartiSex.sign.terms.KS = rbind(PartiSex.sign.terms.KS, PartiSex.GO.signKS)
ParthParti.sign.terms.Fish = rbind(ParthParti.sign.terms.Fish, ParthParti.GO.signFisher)
ParthParti.sign.terms.KS = rbind(ParthParti.sign.terms.KS, ParthParti.GO.signKS)
}
ParthSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthSex.sign.terms.Fish$GO.ID,ParthSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthSex"),
cbind(as.data.frame(table(paste(ParthSex.sign.terms.KS$GO.ID,ParthSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthSex"))
ParthParti.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthParti.sign.terms.Fish$GO.ID,ParthParti.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthParti"),
cbind(as.data.frame(table(paste(ParthParti.sign.terms.KS$GO.ID,ParthParti.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthParti"))
PartiSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(PartiSex.sign.terms.Fish$GO.ID,PartiSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="PartiSex"),
cbind(as.data.frame(table(paste(PartiSex.sign.terms.KS$GO.ID,PartiSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="PartiSex"))
All.GOterms.freq = rbind(ParthSex.GOterms.freq,
ParthParti.GOterms.freq,
PartiSex.GOterms.freq)
#Change name of tables accordingly
write.table(ParthSex.sign.terms.Fish,paste("GO_analysis/ParthSex_GO_",algorithm,"_",fdr.cutoff,"_Fisher.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthSex.sign.terms.KS,paste("GO_analysis/ParthSex_GO_",algorithm,"_",fdr.cutoff,"_KS.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(PartiSex.sign.terms.Fish,paste("GO_analysis/PartiSex_GO_",algorithm,"_",fdr.cutoff,"_Fisher.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(PartiSex.sign.terms.KS,paste("GO_analysis/PartiSex_GO_",algorithm,"_",fdr.cutoff,"_KS.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthParti.sign.terms.Fish,paste("GO_analysis/ParthParti_GO_",algorithm,"_",fdr.cutoff,"_Fisher.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthParti.sign.terms.KS,paste("GO_analysis/ParthParti_GO_",algorithm,"_",fdr.cutoff,"_KS.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(All.GOterms.freq,
paste("GO_analysis/GO_term_frequency_",algorithm,"_",fdr.cutoff,".txt",sep=""),quote = F,row.names = F,sep="\t")
###############################################################
#UPREGULATED GENES
###############################################################
rounds = 100
fdr.cutoff = 0.1
algorithm = "weight01"
ParthSex.sign.terms.Fish = NULL
ParthSex.sign.terms.KS = NULL
PartiSex.sign.terms.Fish = NULL
PartiSex.sign.terms.KS = NULL
ParthParti.sign.terms.Fish = NULL
ParthParti.sign.terms.KS = NULL
for (i in 1:rounds){
print(i)
fbgn.list = strsplit(as.character(all.tab.naEx$primary_FBgn),";")
fbgn.list.random = lapply(fbgn.list, function(x) sample(x,1))
all.tab.naEx.newtab = all.tab.naEx
all.tab.naEx.newtab$primary_FBgn = unlist(fbgn.list.random)
head(all.tab.naEx.newtab)
#Create vactors with padj
ParthSex.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthSex > 0,]$padj.ParthSex)
PartiSex.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.PartiSex > 0,]$padj.PartiSex)
ParthParti.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthParti > 0,]$padj.ParthParti)
names(ParthSex.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthSex > 0,]$primary_FBgn)
names(PartiSex.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.PartiSex > 0,]$primary_FBgn)
names(ParthParti.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthParti > 0,]$primary_FBgn)
#Summarize by taking median
ParthSex.vect = tapply(ParthSex.vect,names(ParthSex.vect),median)
PartiSex.vect = tapply(PartiSex.vect,names(PartiSex.vect),median)
ParthParti.vect = tapply(ParthParti.vect,names(ParthParti.vect),median)
#do GO analysis
ParthSex.GO = top_go_analysis(ParthSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
PartiSex.GO = top_go_analysis(PartiSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
ParthParti.GO = top_go_analysis(ParthParti.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
#add round numbering
ParthSex.GO = lapply(ParthSex.GO, function(x) cbind(x,Round = i))
PartiSex.GO = lapply(PartiSex.GO, function(x) cbind(x,Round = i))
ParthParti.GO = lapply(ParthParti.GO, function(x) cbind(x,Round = i))
#Select significant categories
ParthSex.GO.signFisher = ParthSex.GO$P_Fisher[ParthSex.GO$P_Fisher$FDR < fdr.cutoff,]
ParthSex.GO.signKS = ParthSex.GO$P_KS[ParthSex.GO$P_KS$FDR < fdr.cutoff,]
PartiSex.GO.signFisher = PartiSex.GO$P_Fisher[PartiSex.GO$P_Fisher$FDR < fdr.cutoff,]
PartiSex.GO.signKS = PartiSex.GO$P_KS[PartiSex.GO$P_KS$FDR < fdr.cutoff,]
ParthParti.GO.signFisher = ParthParti.GO$P_Fisher[ParthParti.GO$P_Fisher$FDR < fdr.cutoff,]
ParthParti.GO.signKS = ParthParti.GO$P_KS[ParthParti.GO$P_KS$FDR < fdr.cutoff,]
#Make vector with significant categories
ParthSex.sign.terms.Fish = rbind(ParthSex.sign.terms.Fish, ParthSex.GO.signFisher)
ParthSex.sign.terms.KS = rbind(ParthSex.sign.terms.KS, ParthSex.GO.signKS)
PartiSex.sign.terms.Fish = rbind(PartiSex.sign.terms.Fish, PartiSex.GO.signFisher)
PartiSex.sign.terms.KS = rbind(PartiSex.sign.terms.KS, PartiSex.GO.signKS)
ParthParti.sign.terms.Fish = rbind(ParthParti.sign.terms.Fish, ParthParti.GO.signFisher)
ParthParti.sign.terms.KS = rbind(ParthParti.sign.terms.KS, ParthParti.GO.signKS)
}
ParthSex.GOterms.freq = NULL
ParthParti.GOterms.freq = NULL
PartiSex.GOterms.freq = NULL
All.GOterms.freq = NULL
ParthSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthSex.sign.terms.Fish$GO.ID,ParthSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthSex"),
cbind(as.data.frame(table(paste(ParthSex.sign.terms.KS$GO.ID,ParthSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthSex"))
ParthSex.GOterms.freq
ParthParti.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthParti.sign.terms.Fish$GO.ID,ParthParti.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthParti"),
cbind(as.data.frame(table(paste(ParthParti.sign.terms.KS$GO.ID,ParthParti.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthParti"))
PartiSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(PartiSex.sign.terms.Fish$GO.ID,PartiSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="PartiSex"),
cbind(as.data.frame(table(paste(PartiSex.sign.terms.KS$GO.ID,PartiSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="PartiSex"))
All.GOterms.freq = rbind(ParthSex.GOterms.freq,
ParthParti.GOterms.freq,
PartiSex.GOterms.freq)
###############################################################
#DOWNREGULATED GENES
###############################################################
rounds = 100
fdr.cutoff = 0.1
algorithm = "classic"
ParthSex.sign.terms.Fish = NULL
ParthSex.sign.terms.KS = NULL
PartiSex.sign.terms.Fish = NULL
PartiSex.sign.terms.KS = NULL
ParthParti.sign.terms.Fish = NULL
ParthParti.sign.terms.KS = NULL
for (i in 1:rounds){
print(i)
fbgn.list = strsplit(as.character(all.tab.naEx$primary_FBgn),";")
fbgn.list.random = lapply(fbgn.list, function(x) sample(x,1))
all.tab.naEx.newtab = all.tab.naEx
all.tab.naEx.newtab$primary_FBgn = unlist(fbgn.list.random)
head(all.tab.naEx.newtab)
#Create vactors with padj
ParthSex.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthSex < 0,]$padj.ParthSex)
PartiSex.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.PartiSex < 0,]$padj.PartiSex)
ParthParti.vect = c(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthParti < 0,]$padj.ParthParti)
names(ParthSex.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthSex < 0,]$primary_FBgn)
names(PartiSex.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.PartiSex < 0,]$primary_FBgn)
names(ParthParti.vect) = as.character(all.tab.naEx.newtab[all.tab.naEx.newtab$log2FoldChange.ParthParti < 0,]$primary_FBgn)
#Summarize by taking median
ParthSex.vect = tapply(ParthSex.vect,names(ParthSex.vect),median)
PartiSex.vect = tapply(PartiSex.vect,names(PartiSex.vect),median)
ParthParti.vect = tapply(ParthParti.vect,names(ParthParti.vect),median)
#do GO analysis
ParthSex.GO = top_go_analysis(ParthSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
PartiSex.GO = top_go_analysis(PartiSex.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
ParthParti.GO = top_go_analysis(ParthParti.vect,ontology = "BP", mapping = "org.Dm.eg.db", algorithm = algorithm)
#add round numbering
ParthSex.GO = lapply(ParthSex.GO, function(x) cbind(x,Round = i))
PartiSex.GO = lapply(PartiSex.GO, function(x) cbind(x,Round = i))
ParthParti.GO = lapply(ParthParti.GO, function(x) cbind(x,Round = i))
#Select significant categories
ParthSex.GO.signFisher = ParthSex.GO$P_Fisher[ParthSex.GO$P_Fisher$FDR < fdr.cutoff,]
ParthSex.GO.signKS = ParthSex.GO$P_KS[ParthSex.GO$P_KS$FDR < fdr.cutoff,]
PartiSex.GO.signFisher = PartiSex.GO$P_Fisher[PartiSex.GO$P_Fisher$FDR < fdr.cutoff,]
PartiSex.GO.signKS = PartiSex.GO$P_KS[PartiSex.GO$P_KS$FDR < fdr.cutoff,]
ParthParti.GO.signFisher = ParthParti.GO$P_Fisher[ParthParti.GO$P_Fisher$FDR < fdr.cutoff,]
ParthParti.GO.signKS = ParthParti.GO$P_KS[ParthParti.GO$P_KS$FDR < fdr.cutoff,]
#Make vector with significant categories
ParthSex.sign.terms.Fish = rbind(ParthSex.sign.terms.Fish, ParthSex.GO.signFisher)
ParthSex.sign.terms.KS = rbind(ParthSex.sign.terms.KS, ParthSex.GO.signKS)
PartiSex.sign.terms.Fish = rbind(PartiSex.sign.terms.Fish, PartiSex.GO.signFisher)
PartiSex.sign.terms.KS = rbind(PartiSex.sign.terms.KS, PartiSex.GO.signKS)
ParthParti.sign.terms.Fish = rbind(ParthParti.sign.terms.Fish, ParthParti.GO.signFisher)
ParthParti.sign.terms.KS = rbind(ParthParti.sign.terms.KS, ParthParti.GO.signKS)
}
ParthSex.GOterms.freq = NULL
ParthParti.GOterms.freq = NULL
PartiSex.GOterms.freq = NULL
All.GOterms.freq = NULL
ParthSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthSex.sign.terms.Fish$GO.ID,ParthSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthSex"),
cbind(as.data.frame(table(paste(ParthSex.sign.terms.KS$GO.ID,ParthSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthSex"))
ParthSex.GOterms.freq
ParthParti.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(ParthParti.sign.terms.Fish$GO.ID,ParthParti.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="ParthParti"),
cbind(as.data.frame(table(paste(ParthParti.sign.terms.KS$GO.ID,ParthParti.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="ParthParti"))
PartiSex.GOterms.freq = rbind(
cbind(as.data.frame(table(paste(PartiSex.sign.terms.Fish$GO.ID,PartiSex.sign.terms.Fish$Term,sep="_")) / rounds),
type="Fisher",contrast="PartiSex"),
cbind(as.data.frame(table(paste(PartiSex.sign.terms.KS$GO.ID,PartiSex.sign.terms.KS$Term,sep="_")) / rounds),
type="KS",contrast="PartiSex"))
All.GOterms.freq = rbind(ParthSex.GOterms.freq,
ParthParti.GOterms.freq,
PartiSex.GOterms.freq)
#Change name of tables accordingly
write.table(ParthSex.sign.terms.Fish,paste("GO_analysis/ParthSex_GO_",algorithm,"_",fdr.cutoff,"_Fisher_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthSex.sign.terms.KS,paste("GO_analysis/ParthSex_GO_",algorithm,"_",fdr.cutoff,"_KS_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(PartiSex.sign.terms.Fish,paste("GO_analysis/PartiSex_GO_",algorithm,"_",fdr.cutoff,"_Fisher_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(PartiSex.sign.terms.KS,paste("GO_analysis/PartiSex_GO_",algorithm,"_",fdr.cutoff,"_KS_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthParti.sign.terms.Fish,paste("GO_analysis/ParthParti_GO_",algorithm,"_",fdr.cutoff,"_Fisher_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(ParthParti.sign.terms.KS,paste("GO_analysis/ParthParti_GO_",algorithm,"_",fdr.cutoff,"_KS_down.txt",sep=""),quote = F,row.names = F,sep="\t")
write.table(All.GOterms.freq,
paste("GO_analysis/GO_term_frequency_",algorithm,"_",fdr.cutoff,"_down.txt",sep=""),quote = F,row.names = F,sep="\t")