How to use enrichGSEA_pip.r in R language
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EnrichGSEA_pip.R GSEA enrichment analysis
Instructions: $Rscript $scriptdir/enrichGSEA_pip.r-husage: / work/my_stad_immu/scripts/enrichGSEA_pip.r [- h]-an all.deg.file-g gmtfile [- p pvalueCutoff] [- t pvalueCutoff] [- n prefix] [- o outdir] [- H height] [- W width] GSEA enrich analysis: https://www..com/article/1504optional arguments:-h -- help show this help message and exit-an all.deg.file,-- all.deg.file all.deg.file all diff express gene list file,must include log2FC column, required-g gmtfile,-- gmtfile gmtfile GSEA gmtfile function class file, required-p pvalueCutoff,-- pvalueCutoff pvalueCutoff pvalue cutoff on enrichment tests to report [optional, default: 0.1]-t top,-- top NES for barplot [optional, default:10]-n prefix,-- prefix prefix the output file prefix [optional, default: GSEA]-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 5] parameter description:
-an enter the results of differential gene analysis; must contain the differential multiple information of log2FC, which can be used for GSEA sequencing.
-g specify gmt file gene set: more GSEA functional enrichment data download: http://software.broadinstitute.org/gsea/downloads.jsp#msigdb
Use examples: # more GSEA feature enrichment data download: http://software.broadinstitute.org/gsea/downloads.jsp#msigdbwget-c https://data.broadinstitute.org/gsea-msigdb/msigdb/release/7.4/c2.cp.kegg.v7.4.symbols.gmtRscript $scriptdir/enrichGSEA_pip.r-- all.deg.file $workdir/04.deg/S1_vs_S2.all.tsv\-- gmtfile c2.cp.kegg.v7.4.symbols.gmt -o GSEA-n S1_vs_S2_KEGG-p 0.05 to this point The study on "how to use enrichGSEA_pip.r in R language" is over. I hope to be able to solve your doubts. The collocation of theory and practice can better help you learn, go and try it! If you want to continue to learn more related knowledge, please continue to follow the website, the editor will continue to work hard to bring you more practical articles!
