基因功能富集分析-R语言
时间:2022-05-04
本文章向大家介绍基因功能富集分析-R语言,主要内容包括其使用实例、应用技巧、基本知识点总结和需要注意事项,具有一定的参考价值,需要的朋友可以参考一下。
##安装bioconductor上的包;
source(“http://bioconductor.org/biocLite.R”)
biocLite(“clusterprofiler”)
biocLite("org.Hs.eg.db")#人基因名称等信息包;
##加载clusterprofiler包到当前工作路径;
library(clusterprofiler)#基因富集分析用;
library(org.Hs.eg.db)
#读入需要分析的数据,包含一列基因名称的列表;
a <- read.table(file.choose(),header = F,colClasses = "character")
#a <- read.table(file.choose(),header = F,colClasses = c("V1"= "character")),只设置第一列值为字符型;
###选取基因列的所有行
b <- a[,1]
###利用bitr函数将基因名称转换为ENTREZID号;物种是人org.Hs.eg.db;
eg = bitr(b,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = "org.Hs.eg.db")
#可能会有部分基因对应不到ENTREZID,0.4% of input gene IDs are fail to map...
###转换后的基因名称保存为文档;
write.table(eg,file = "test_id.txt")
gene <- eg[,2]
###进行GO和KEGG分析;
library(clusterProfiler)
library(org.Hs.eg.db)
a <- read.table(file.choose(),header = F,colClasses = c("V1"= "character"))
b <- a[,1]
eg <- bitr(b,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = "org.Hs.eg.db")
gene <- eg[,2]
ego_CC <- enrichGO(gene = gene,
OrgDb=org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
minGSSize = 1,
pvalueCutoff = 0.01,
qvalueCutoff = 0.01,
readable = TRUE)
write.csv(as.data.frame(ego_CC),row.names = F, file = "ego_CC.csv")
barplot(ego_CC,drop = TRUE,title = "enrichment_CC",showCategory = 12)
ego_BP <- enrichGO(gene = gene,
OrgDb=org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
minGSSize = 1,
pvalueCutoff = 0.01,
qvalueCutoff = 0.01,
readable = TRUE)
write.csv(as.data.frame(ego_BP),row.names = F, file = "ego_BP.csv")
barplot(ego_BP,drop = TRUE,title = "enrichment_BP",showCategory = 12)
ego_MF <- enrichGO(gene = gene,
OrgDb=org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
minGSSize = 1,
pvalueCutoff = 0.01,
qvalueCutoff = 0.01,
readable = TRUE)
write.csv(as.data.frame(ego_MF),row.names = F, file = "ego_MF.csv")
barplot(ego_MF,drop = TRUE,title = "enrichment_MF",showCategory = 12)
kk <- enrichKEGG(gene = gene,
organism ="hsa",
pvalueCutoff = 0.01,
qvalueCutoff = 0.01,
minGSSize = 1,
#readable = TRUE ,
use_internal_data = FALSE)
write.csv(as.data.frame(kk),row.names = F, file = "kk.csv")
barplot(kk,drop = TRUE,title = "enrichment_kegg",showCategory = 12)
###DisGeNET4 is an integrative and comprehensive resources of gene-disease associations from several public data sources and the literature. It contains gene-disease associations and snp-gene-disease associations.
###The enrichment analysis of disease-gene associations is supported by the enrichDGN function and analysis of snp-gene-disease associations is supported by the enrichDGNv function.
dgn <- enrichDGN(gene = gene,
pAdjustMethod = "BH",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
readable = TRUE)
head(dgn)
write.csv(as.data.frame(dgn),row.names = F, file = "dgn.csv")
barplot(dgn,drop = TRUE,title = "enrichment_disease",showCategory = 12)
###条行图,按p值从小到大排列;
barplot(ego_CC,showCategory = 24,title = "EnrichmentGO_CC")
###点状图,按富集数从大到小进行排列;
dotplot(ego_CC,title = "EnrichenmentGo_CC")
Gene Ontology富集分析结果表格。
GO ID: Gene Ontology数据库中唯一的标号信息
Description :Gene Ontology功能的描述信息
GeneRatio:输入基因中与该Term相关的基因数与整个输入基因总数的比值
BgRation:所有background基因中与该Term相关的基因数与所有background基因的比值
pvalue: 富集分析统计学显著水平,一般情况下, P-value < 0.05 该功能为富集项
p.adjust 矫正后的P-Value
qvalue:对p值进行统计学检验的q值
Count:差异基因中与该Term相关的基因数
http://scu.zju.edu.cn/redir.php?catalog_id=58400&object_id=203725
http://www.bioconductor.org/packages/release/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
http://www.bio-info-trainee.com/370.html
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