How to use enrichGO_pip.r in R language
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EnrichGO_pip.R GO enrichment analysis
Instructions for using Rscript $scriptdir/enrichGO_pip.r-husage: / 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] [- n prefix] [- o outdir] [- H height] [- W width] GO enrich analysis:optional 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]-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 GO Category to show, [optional, default: 10]-n prefix -- prefix prefix the output file prefix [optional, default: enrichGO]-o outdir,-- outdir outdir output file directory [default cwd]-H height,-- height height the height of pic inches [default 10]-W width,-- width width the width of pic inches [default 10] 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/enrichGO_pip.r-- gene.list $workdir/04.deg/S1_vs_S2.DEG.final.tsv\-o GO-n S1_vs_S2-- pvalueCutoff 0.5-- ann.db org.Hs.eg.db\-- idtype SYMBOL is all the content of this article "how to use enrichGO_pip.r in R language". Thank you for reading! I believe you will gain a lot after reading this article. The editor will update different knowledge for you every day. If you want to learn more knowledge, please pay attention to the industry information channel.
