--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ReactomePA.R	Thu May 20 08:39:40 2021 +0000
@@ -0,0 +1,132 @@
+###############################################################################
+#title: Reactome Pathway enrich Analysis of a gene set
+#author: xiaowei
+# time: Mar.31 2021
+###############################################################################
+
+
+#####################
+#Input argument for this function
+#####################
+# title
+  # Reactome Pathway enrich Analysis of a gene set
+
+# description
+  #Input a vector of all different expression gene and Output the enriched Significant Reactome Pathways
+
+# basic input: 
+  # genelist, g, 1, character, an csv file contained all different expression genes with entrez gene id, and has one column as DEgenes
+
+# Optional:
+  # pvalueCutoff  , p , 1, numeric  , Cutoff value of p-value,
+  # organism      , o , 1, character, one of 'human', 'rat', 'mouse', 'celegans', 'yeast', 'zebrafish' and 'fly',
+  # pAdjustMethod , w , 1, character, one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none',
+  # minGSSize     , i , 1, integer  , minimal size of genes annotated by Ontology term for testing,
+  # maxGSSize     , a , 1, integer  , maximal size of each geneSet for analyzing,
+  # convertId     , c , 0, logical  , whether papping gene ID to gene Name,
+
+
+# OUT:
+  # sigP, s, 1, character, output csv file name
+
+##############################################################################
+#Input argument
+###############################################################################
+#args <- commandArgs(trailingOnly = TRUE)
+
+spec <- matrix(c("genelist", "g", 1, "character", "an csv file contained all different expression genes with entrez gene id",
+                 "pvalueCutoff", "p", 1, "numeric", "Cutoff value of p-value",
+                 "organism", "o", 1, "character", "one of 'human', 'rat', 'mouse', 'celegans', 'yeast', 'zebrafish' and 'fly'",
+                 "pAdjustMethod","w", 1, "character", "one of 'holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none'",
+                 "minGSSize", "i",1, "integer", "minimal size of genes annotated by Ontology term for testing",
+                 "maxGSSize", "a",1, "integer", "maximal size of each geneSet for analyzing",
+                 "convertId", "c",0, "logical", "whether papping gene ID to gene Name",
+                 "sigP", "s", 1, "character", "output csv file name"),
+               byrow = TRUE, ncol = 5)
+
+
+if (!requireNamespace("getopt", quietly = TRUE))
+  install.packages("getopt")
+
+
+opt <- getopt::getopt(spec)
+
+#-------整理输入的参数----------------
+de <- opt$genelist 
+if(is.null(opt$pvalueCutoff)){
+  pvalueCutoff = 0.05
+}else{
+  pvalueCutoff <- opt$pvalueCutoff
+}
+
+if(is.null(opt$organism)){
+  organism <- "human"
+}else{
+  organism <- opt$organism
+}
+
+if(is.null(opt$pAdjustMethod)){
+  pAdjustMethod <- "BH"
+}else{
+  pAdjustMethod <- opt$pAdjustMethod  
+}
+
+if(is.null(opt$minGSSize)){
+  minGSSize <- 10
+}else{
+  minGSSize <- opt$minGSSize  
+}
+
+if(is.null(opt$maxGSSize)){
+  maxGSSize <- 500
+}else{
+  maxGSSize <- opt$maxGSSize  
+}
+
+
+if(is.null(opt$convertId)){
+  convertId <- FALSE
+}else{
+  convertId <- opt$convertId
+}
+
+if(is.null(opt$sigP)){
+  opt$sigP <- "Significant_Reactome_Pathway_result.csv"
+}
+
+###############################################################################
+#运行代码
+###############################################################################
+de <- read.csv(de)
+de <- de$DEgenes
+
+suppressPackageStartupMessages(
+  if (!requireNamespace("ReactomePA", quietly = TRUE)){
+    if (!requireNamespace("BiocManager", quietly = TRUE))
+      install.packages("BiocManager")
+    BiocManager::install("ReactomePA")
+  })
+
+#suppressPackageStartupMessages(library(ReactomePA))
+
+#Pathway Enrichment Analysis of a gene set
+result_sigP <- ReactomePA::enrichPathway(gene=de, #entrez id 的基因 向量
+                             pvalueCutoff= pvalueCutoff,  #p值阈值
+                             organism = organism, #有机体是"human"、"rat"、"mouse"、"celegans"、"yeast"、"zebrafish"、"fly"其中一个
+                             pAdjustMethod = pAdjustMethod, #"holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" 其中一个
+                             #unverse, #背景基因
+                             minGSSize = minGSSize, #检验本体术语时，限制最少基因个数
+                             maxGSSize = maxGSSize, #分析基因集时，限制最大基因个数
+                             readable=convertId) #是否将geneID映射到基因名称
+
+result_sigP <- as.data.frame(result_sigP)
+
+
+
+###############################################################################
+#输出
+###############################################################################
+write.csv(result_sigP, file = opt$sigP, row.names = FALSE)
+
+
+