总结来说,enrichGO 和 gseGO 适用于不同的分析场景,具体选择要根据数据特点和研究目标决定。如果你关注差异基因的具体功能,enrichGO 更适合;如果你希望从整体趋势分析所有基因的功能分布,gseGO 是更好的选择。 在进行gseGO分析时,你可以通过以下方法设置条件,控制基因数量,避免基因数太少或太多对分析结果产生影响: ...
不过后续的enrichGO函数的参数keyType就要改一下。 (2)GO<-enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 10, maxGSSize = 500,readable = FALSE,pool = FALSE) ——gene :就是需要基因名的...
本文用clusterProfiler包GO富集分析,分别用enrichplot和ggplot2绘图,并用GOplot包绘制Bubble图、Circle图、Heat图、Chord图。 1用DOSE包里的基因list为例 library("DOSE") data(geneList, package = "DOSE") g_list <- names(geneList)[1:100] head(g_list) [1] "4312" "8318" "10874" "55143" "55388...
go_enrich$Description[i]=description_collapse go_enrich$Description=gsub(pattern = "NA","",go_enrich$Description) #gsub()可以用于字段的删减、增补、替换和切割,可以处理一个字段也可以处理由字段组成的向量。gsub(“目标字符”, “替换字符”, 对象) } #转成因子,防止重新排列 #go_enrich$type_order=f...
enrichgo函数 在现代编程语言中,函数是一种非常重要的概念。函数是一段可以被重复使用的代码块,它可以接受输入参数并返回输出结果。函数的使用可以使代码更加简洁、易于维护和重用。在Go语言中,函数也是一项重要的特性。Go语言的函数可以被用来实现各种不同的任务,从简单的数学计算到网络通信和并发编程。 在本文中,...
enrichGO出不来结果？没结果也是正确的结果Dear Dr. Guangchuang Yu, I write to you regarding a doubt concerning the enrichGO function from Clustalprofiler package. I have been used this package before, but now I’m using the same R script and I have an error message.This is the command I ...
enrichGO_pip.R GO富集分析 使用说明 Rscript$scriptdir/enrichGO_pip.r-h usage:/work/my_stad_immu/scripts/enrichGO_pip.r [-h]-g gene.list [-d ann.db] [-t idtype] [-s show.type] [-p pvalueCutoff] [-q qvalueCutoff] [-c showCategory] [-nprefix] ...
go <- enrichGO(gene = id, #universe = names(geneList),#背景基因 OrgDb = "org.Mm.eg.db", ont = "ALL",#"BP", "MF", "CC" pAdjustMethod = "BH", pvalueCutoff = 0.5, qvalueCutoff = 0.5, readable = TRUE) Error in data.frame(..., check.names = FALSE) : 行名里有缺失值 ...
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enrichGO_pip.R GO富集分析 使用说明 Rscript $scriptdir/enrichGO_pip.r -h usage: /work/my_stad_immu/scripts/enrichGO_pip.r [-h] -g gene.list [-d ann.db] [-t idtype] [-s show.type] [-p pvalueCutoff] [-q qvalueCutoff] ...