In barzine/barzinePhdR: Code developed while and for my PhD thesis at the EMBL-EBI

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

library(barzinePhdR)
library(barzinePhdData)

data("pandey.ppkm")
data("uhlen.htseq.fpkm.pooled")
data("gtex.htseq.fpkm.pooled")

data("g.Pcoding")

genesList<-union(g.Pcoding,rownames(pandey.ppkm))

pandey <- strip(pandey.ppkm)
uhlen  <- strip(uhlen.htseq.fpkm.pooled)
gtex   <- strip(gtex.htseq.fpkm.pooled)


uhlen<-uhlen[rownames(uhlen) %in% genesList,]
gtex<-gtex[rownames(gtex) %in% genesList,]

comCond<-Intersect(colnames(pandey),colnames(uhlen),colnames(gtex))
comCond


pandey <- pandey[,comCond]
uhlen  <- uhlen[,comCond]
gtex   <- gtex[,comCond]


uhlen<-crudeStrip(uhlen,1)
gtex<-crudeStrip(gtex,1)

pandey.spe <- selectSpecific(pandey)
uhlen.spe  <- selectSpecific(uhlen,threshold=1)
gtex.spe   <- selectSpecific(gtex,threshold=1)

List[Spe_pandey_uhlen_OverlapPercent,Spe_pandey_uhlen_OverlappValue]<-matrix.overlap_res(pandey.spe,uhlen.spe,report="")

barzine/barzinePhdR documentation built on Nov. 23, 2024, 8:54 p.m.