2021-12-24 KEGG
2021-12-30 本文已影响0人
千容安
对于报错：
None of the keys entered are valid keys for 'SYMBOL'.
重新修改代码：
setwd("C:\\Users\\Administrator.DESKTOP-4UQ3Q0K\\Desktop")
library(clusterProfiler)
library("readxl")
d<-read.csv("mk_fm_grp2all.csv")
names(geneList) <- as.character(d[,1])
geneList<-rownames(d)
library(org.Mm.eg.db)
library(org.Hs.eg.db)
library(AnnotationHub)
library(dbplyr)
library(BiocFileCache)
geneList <- sort(geneList, decreasing = TRUE)
geneList = d$X
此时的geneList：
geneEntrezID <- bitr(geneList, fromType="SYMBOL", toType=c("ENTREZID","UNIPROT"), OrgDb="org.Hs.eg.db")
成功：
'select()' returned 1:many mapping between keys and columns
Warning message:
In bitr(geneList, fromType = "SYMBOL", toType = c("ENTREZID", "UNIPROT"), :
17.38% of input gene IDs are fail to map...
kk <- enrichKEGG(gene= geneEntrezID[,2],organism= 'human',pvalueCutoff = 0.05)
head(kk)
browseKEGG(kk, 'hsa04066')
第二次输入browseKEGG(kk, 'hsa04066')，就没有反应了，浏览器里也没有图，解决方式：
在网址里修改，改为所需的hsa04066
image.png
