clusterProfiler
clusterProfiler也是通过KEGG API去获取物种对应的pathway注释,对于已有pathway注释的物种,我们只需要知道对应的三字母缩写, clusterProfiler就会联网自动获取该物种的pathway注释信息。
pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500,
qvalueCutoff = 0.2, use_internal_data = FALSE)
- keyType:one of "kegg",’ncbi-geneid’,’ncib-proteinid’ and ’uniprot’
- use_internal_data=FALSE:logical, use KEGG.db or latest online KEGG data
remotes::install_github("YuLab-SMU/createKEGGdb")
library(createKEGGdb)
create_kegg_db("dme")
install.packages("KEGG.db_1.0.tar.gz",repos=NULL,type="source")
library(KEGG.db)
ERROR: unable to collate and parse R files for package 'createKEGGdb'
* removing 'E:/Eprogramfiles/R/R-3.6.3/library/createKEGGdb'
Error: Failed to install 'createKEGGdb' from GitHub:
yum install libcurl-devel
yum install openssl
yum install openssl-devel
yum install libxml2
yum install libxml2-devel
wget https://cran.r-project.org/src/contrib/Archive/RcppArmadillo/RcppArmadillo_0.9.900.3.0.tar.gz
R CMD INSTALL -l /usr/lib64/R/library RcppArmadillo_0.9.900.3.0.tar.gz
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("clusterProfiler")
BiocManager::install("topGO")
BiocManager::install("org.Hs.eg.db")
BiocManager::install("org.Mm.eg.db")
链接:https://www.jianshu.com/p/d484003dced5
https://github.com/YuLab-SMU/createKEGGdb/issues/4
https://bioconductor.org/packages/3.10/data/annotation/src/contrib/org.Hs.eg.db_3.10.0.tar.gz
https://bioconductor.org/packages/3.10/data/annotation/src/contrib/org.Mm.eg.db_3.10.0.tar.gz