How to use enrichKEGG_pip.r in R language
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EnrichKEGG_pip.r KEGG enrichment analysis
Instructions for use: $Rscript $scriptdir/enrichKEGG_pip.r-husage: / work/my_stad_immu/scripts/enrichKEGG_pip.r [- h]-g gene.list [- d ann.db] [- t idtype] [- s show.type] [- O organism] [- p pvalueCutoff] [- Q qvalueCutoff] [- c showCategory] [- n prefix] [- o outdir] [- H height] [- W width] KEGG enrich analysis: https://www..com/article/1503optional arguments:-h -- help show this help message and exit-g gene.list,-- gene.list gene.list diff expressed gene list file, required-d ann.db,-- ann.db ann.db org.Hs.eg.db or org.Mm.eg.db, for more info visit: https://www..com/article/1244 [optional Default: org.Hs.eg.db]-t idtype,-- idtype idtype deg gene idtype: ENSEMBL SYMBOL ENTREZID GENENAME [optional, default: SYMBOL]-s show.type,-- show.type show.type set example ID type name [optional, default: ENTREZID]-O organism -- organism, for more info visit: https://www..com/article/787 [optional, default: hsa]-- p pvalueCutoff,-- pvalueCutoff pvalueCutoff pvalue cutoff on enrichment tests to report, [optional, default: 0.05]-Q qvalueCutoff -- qvalueCutoff qvalueCutoff qvalue cutoff on enrichment tests to report as significant. Tests must pass i) pvalueCutoff on unadjusted pvalues, ii) pvalueCutoff on adjusted pvalues and iii) qvalueCutoff on qvalues to be reported., [optional, default: 0.2]-c showCategory,-- showCategory showCategory how many KEGG Category to show, [optional, default: 10]-n prefix -- prefix prefix the output file prefix [optional, default: KEGG]-o outdir,-- outdir outdir output file directory [default cwd]-H height,-- height height the height of pic inches [default 5]-W width,-- width width the width of pic inches [default 7] parameter description:
-g enter the gene list file: the script reads the first column of gene ID as the gene set:
-d species annotation database: human: org.Hs.eg.db
-t specifies the ID type of the input gene list
Use examples: Rscript $scriptdir/enrichKEGG_pip.r-- gene.list $workdir/04.deg/S1_vs_S2.DEG.final.tsv\-o KEGG-n S1_vs_S2-- pvalueCutoff 0.01-- ann.db org.Hs.eg.db-- organism hsa\-- idtype SYMBOL here, this article "how to use enrichKEGG_pip.r in R language" has been introduced. If you want to master the knowledge of this article, you still need to practice and use it. If you want to know more about the articles, you are welcome to follow the industry information channel.
