| -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. |