代码本中参考代码：

cd $workdir/

mkdir 6.enrich

cd 6.enrich

#GO,KEGG 富集分析以下脚本只支持模式物种见表格：https://www.omicsclass.com/article/1244

#非模式物种参考：http://guangchuangyu.github.io/cn/2017/07/clusterprofiler-maize/

Rscript $scriptdir/enrichKEGG_pip.R --deg.file $workdir/5.deg/normal_vs_tumor.DEG.final.tsv -o KEGG -n normal_vs_tumor --pvalueCutoff 1 --ann.db org.Hs.eg.db --organism hsa --idtype ENSEMBL --totype ENTREZID 
输入标黄代码后，出现如下错误：

[root@bdc6beb897b9  16:59:07 /work/zhaoran/6.enrich]#Rscript $scriptdir/enrichKEGG_pip.R --deg.file $workdir/5.deg/normal_vs_tumor.DEG.final.tsv -o KEGG -n normal_vs_tumor --pvalueCutoff 1 --ann.db org.Hs.eg.db --organism hsa --idtype ENSEMBL --totype ENTREZID

--> Q&A for bioinformatics, please visit the website: www.omicsclass.com

--> Recommended to learn R language:

--> https://study.163.com/course/introduction/1209073807.htm?share=1&shareId=1030291076

 

Registered S3 method overwritten by 'enrichplot':

  method               from

  fortify.enrichResult DOSE

clusterProfiler v3.14.3  For help: https://guangchuangyu.github.io/software/clusterProfiler

 

If you use clusterProfiler in published research, please cite:

Guangchuang Yu, Li-Gen Wang, Yanyan Han, Qing-Yu He. clusterProfiler: an R package for comparing biological themes among gene clusters. OMICS: A Journal of Integrative Biology. 2012, 16(5):284-287.

DOSE v3.12.0  For help: https://guangchuangyu.github.io/software/DOSE

 

If you use DOSE in published research, please cite:

Guangchuang Yu, Li-Gen Wang, Guang-Rong Yan, Qing-Yu He. DOSE: an R/Bioconductor package for Disease Ontology Semantic and Enrichment analysis. Bioinformatics 2015, 31(4):608-609

 

Loading required package: org.Hs.eg.db

Loading required package: AnnotationDbi

Loading required package: stats4

Loading required package: BiocGenerics

Loading required package: parallel

 

Attaching package: ‘BiocGenerics’

 

The following objects are masked from ‘package:parallel’:

 

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,

    clusterExport, clusterMap, parApply, parCapply, parLapply,

    parLapplyLB, parRapply, parSapply, parSapplyLB

 

The following objects are masked from ‘package:stats’:

 

    IQR, mad, sd, var, xtabs

 

The following objects are masked from ‘package:base’:

 

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,

    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,

    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,

    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,

    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,

    union, unique, unsplit, which, which.max, which.min

 

Loading required package: Biobase

Welcome to Bioconductor

 

    Vignettes contain introductory material; view with

    'browseVignettes()'. To cite Bioconductor, see

    'citation("Biobase")', and for packages 'citation("pkgname")'.

 

Loading required package: IRanges

Loading required package: S4Vectors

 

Attaching package: ‘S4Vectors’

 

The following object is masked from ‘package:base’:

 

    expand.grid

 

 

##############################################################################

Pathview is an open source software package distributed under GNU General

Public License version 3 (GPLv3). Details of GPLv3 is available at

http://www.gnu.org/licenses/gpl-3.0.html. Particullary, users are required to

formally cite the original Pathview paper (not just mention it) in publications

or products. For details, do citation("pathview") within R.

 

The pathview downloads and uses KEGG data. Non-academic uses may require a KEGG

license agreement (details at http://www.kegg.jp/kegg/legal.html).

##############################################################################

please set right --idtype you input to analysis, The example ID types below are supported:

 [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"

 [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"

[11] "GO"           "GOALL"        "IPI"          "MAP"          "OMIM"

[16] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"

[21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"       "UNIGENE"

[26] "UNIPROT"

Warning: You have selected the following columns that can have a many to one

  relationship with the primary key: ACCNUM, ALIAS, ENSEMBL,

  ENSEMBLPROT, ENSEMBLTRANS, IPI, MAP, OMIM, PFAM, PROSITE, UCSCKG,

  UNIGENE, UNIPROT . Because you have selected more than a few such

  columns there is a risk that this selection may balloon up into a

  very large result as the number of rows returned multiplies

  accordingly. To experience smaller/more manageable results and faster

  retrieval times, you might want to consider selecting these columns

  separately.

 'select()' returned 1:many mapping between keys and columns

  ENTREZID   ACCNUM ALIAS         ENSEMBL ENSEMBLPROT ENSEMBLTRANS         IPI

1        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

2        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

3        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

4        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

5        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

6        1 AA484435   A1B ENSG00000121410        <NA>         <NA> IPI00022895

       MAP   OMIM    PFAM PROSITE SYMBOL            UCSCKG   UNIGENE UNIPROT

1 19q13.43 138670 PF13895 PS50835   A1BG ENST00000596924.1 Hs.529161  P04217

2 19q13.43 138670 PF13895 PS50835   A1BG ENST00000596924.1 Hs.529161  V9HWD8

3 19q13.43 138670 PF13895 PS50835   A1BG ENST00000596924.1 Hs.709582  P04217

4 19q13.43 138670 PF13895 PS50835   A1BG ENST00000596924.1 Hs.709582  V9HWD8

5 19q13.43 138670 PF13895 PS50835   A1BG ENST00000263100.7 Hs.529161  P04217

6 19q13.43 138670 PF13895 PS50835   A1BG ENST00000263100.7 Hs.529161  V9HWD8

 [ reached 'max' / getOption("max.print") -- omitted 383423 rows ]

'select()' returned 1:many mapping between keys and columns

Warning message:

In bitr(DEG_list, fromType = opt$idtype, toType = opt$totype, OrgDb = opt$ann.db) :

  26.02% of input gene IDs are fail to map...

 Error in download.KEGG.Path(species) :

  'species' should be one of organisms listed in 'http://www.genome.jp/kegg/catalog/org_list.html'...

Calls: enrichKEGG ... prepare_KEGG -> download_KEGG -> download.KEGG.Path

Execution halted