Skip to main content
. Author manuscript; available in PMC: 2019 Nov 19.
Published in final edited form as: Nat Protoc. 2019 Feb 1;14(3):756–780. doi: 10.1038/s41596-018-0113-7
-top An integer, specifying the number of top selected genes labeled in rank figure.
-bottom An integer, specifying the number of bottom selected genes labeled in rank figure.
-interstGenes A character vector, specifying the genes of interest labeled in rank figure
-pvalueCutoff A numeric, specifying the FDR cutoff of enrichment analysis.
-adjust One of “holm”, “hochberg”, “hommel”, “bonferroni”, “BH”, “BY”, “fdr”, “none”.
-enrich_kegg One of “ORT”(Over-Representing Test), “GSEA”(Gene Set Enrichment Analysis), “DAVID”, “GOstats”, and “HGT”(HyperGemetric test), or index from 1 to 5, specifying the enrichment method used for kegg enrichment analysis.
-gsea A boolean value that indicates whether GSEA analysis is performed.
-posControl A file path or a character vector, specifying the positive control genes used for cell cycle normalization, if NULL, use build-in essential gene list.
-loess Boolean, specify whether to include loess normalization in the pipeline.
-view_allpath Boolean, specify if all pathway view figures are output.
-outdir Output directory on disk.