GSEA_GeneSets_ID2Symbol.Rmd

---
title: "GSEA_GeneSets_Normalize2Symbol"
author: "Botao Wang"
date: "2022-09-26"
output: html_document

params:
  workdir: "E:\\PostGraduate\\Botao\\Code_Verification\\SignatureGenes_GO-PW_Correlation"
  libdir: "E:\\Code_Example\\R\\GeneSignature\\GeneSignature-Pathways_Correlation\\lib"
  resultsdir: ".\\results\\"
  picdir: ".\\pics\\"
  
  GOGeneset: ".\\data\\c5.go.v2022.1.Hs.entrez.gmt"
  PWGeneset: ".\\data\\c2.cp.v2022.1.Hs.entrez.gmt"
  GeneNameAnno: ".\\data\\Homo_sapiens.gene_info.csv"
  
---

```{r setup, include=FALSE}
# rm(list = ls())
# .rs.restartR()

library("knitr")
# library("limma")
# library("ComplexHeatmap")
# library("circlize")

knitr::opts_chunk$set(echo = TRUE)
#* HTML显示结果时同时显示代码

file.exists(params$workdir)
knitr::opts_knit$set(root.dir = params$workdir)
#* 设定工作目录
getwd()

source(file.path(params$lib, "GeneSignature-Pathways_Correlation_Function.R"))

```

## Prepare data

```{r Preparation}

# Read in Gene Sets from GO&PW
goGeneSet <- readGMT(params$GOGeneset)
pathwayGeneSet <- readGMT(params$PWGeneset)

# Read in Gene Name Annotation
geneNameAnno <- read.csv(params$GeneNameAnno, check.names = F)

```

## Gene Name Conversion


```{r GeneName Conversion}

#===============================================================================
#---------------------------- Gene ID Conversion -------------------------------
#===============================================================================


# GO Gene-Sets ID Convert to Symbol
#===============================================================================

goGeneSet_new <- goGeneSet
message("提示：正在将ID统一规范为Symbol：")
progressBar <- txtProgressBar(style=3)
setNum <- 1
geneNum <- 0
for (i in 1:length(goGeneSet)){
  setTxtProgressBar(progressBar, setNum/length(goGeneSet))
  
  for (j in 1:length(goGeneSet[[i]])){
    position <- which(geneNameAnno$GeneID == goGeneSet[[i]][j])
    goGeneSet_new[[i]][j] <- geneNameAnno$Symbol[position]
    
    geneNum <- geneNum+1
  }
  setNum <- setNum+1
}
close(progressBar)
message(paste("完成！GO共转换了", setNum, "个基因集，共转换了", geneNum, "个基因ID"))

# Pathway Gene-Sets ID Convert to Symbol
#===============================================================================

pathwayGeneSet_new <- pathwayGeneSet
message("提示：正在将ID统一规范为Symbol：")
progressBar <- txtProgressBar(style=3)
setNum <- 1
geneNum <- 0
for (i in 1:length(pathwayGeneSet)){
  setTxtProgressBar(progressBar, setNum/length(pathwayGeneSet))
  
  for (j in 1:length(pathwayGeneSet[[i]])){
    position <- which(geneNameAnno$GeneID == pathwayGeneSet[[i]][j])
    pathwayGeneSet_new[[i]][j] <- geneNameAnno$Symbol[position]
    
    geneNum <- geneNum+1
  }
  setNum <- setNum+1
}
close(progressBar)
message(paste("完成！Pathway共转换了", setNum, "个基因集，共转换了", geneNum, "个基因ID"))


```



```{r save result}


# save go Gene set
#===============================================================================
goGeneSet_normalized_file <- file.path(params$workdir ,params$resultsdir, "goGeneSet_normalized.gmt")
file.create(goGeneSet_normalized_file)

for (i in 1:length(goGeneSet_new)){
  goGeneSet_new[[i]][length(goGeneSet_new[[i]])] <- paste(goGeneSet_new[[i]][length(goGeneSet_new[[i]])], "\n", sep="")
  
  line <- c(names(goGeneSet_new)[i], goGeneSet_new[[i]])
  cat(line, file=goGeneSet_normalized_file, append=TRUE, sep="\t", fill=FALSE)
}


# save pathway Gene set
#===============================================================================

pathwayGeneSet_normalized_file <- file.path(params$workdir ,params$resultsdir, "pathwayGeneSet_normalized.gmt")
file.create(pathwayGeneSet_normalized_file)

for (i in 1:length(pathwayGeneSet_new)){
  pathwayGeneSet_new[[i]][length(pathwayGeneSet_new[[i]])] <- paste(pathwayGeneSet_new[[i]][length(pathwayGeneSet_new[[i]])], "\n", sep="")
  
  line <- c(names(pathwayGeneSet_new)[i], pathwayGeneSet_new[[i]])
  cat(line, file=pathwayGeneSet_normalized_file, append=TRUE, sep="\t", fill=FALSE)
}

```