filejoincode.R

library(sqldf)
Clinvar<-read.delim("clinvar_genes_phenos_updated_grouped.txt")
Global<-read.delim("mgi_Phenotype.txt" ,header=FALSE )
Disease<-read.delim("NHGRI.signGene.list")

Clinvar<-Clinvar[,c(2,5)]
colnames(Clinvar)<-colnames(Disease)
Disease<-rbind(Disease,Clinvar)


colnames(Global)<-c("HGS","HGN","MGN","MGS","Phenotype")

Mergetable<-sqldf('select a.*,b.* from Global a join Disease b on a.HGN=b.gene')

D<-unique(Disease[,2])
G<-unique(Global[,5])
x<-expand.grid(D[!is.na(D)],G[!is.na(G)])
x1<-sqldf('select a.Var1, a.Var2, count(b.HGS) as Overlap 
        from x a join Mergetable b on a.Var1=b.trait and a.Var2=b.Phenotype
          group by a.Var1, a.Var2')

x2<-sqldf('select a.Var1, a.Var2, Overlap, count(b.HGS) as DiseaseOnly 
        from x1 a left join Mergetable b on a.Var1=b.trait where a.Var2<>b.Phenotype
          group by a.Var1, b.Var2, a.Overlap')

x3<-sqldf('select a.Var1, a.Var2, Overlap, DiseaseOnly, count(b.HGS) as PhenotypeOnly 
        from x2 a left join Mergetable b on a.Var2=b.Phenotype where a.Var1<>b.trait
          group by a.Var1, a.Var2, a.Overlap, a.DiseaseOnly')
save(x3, file="Contingency.Rda")