msigdb_gsea {GenomicSuperSignature} | R Documentation

## MSigDB GSEA results

### Description

MSigDB GSEA results

### Usage

    msigdb_gsea(
      ind,
      RAVmodel,
      category = "C2",
      n = NULL,
      pvalueCutoff = 0.5,
      minGSSize = 10,
      maxGSSize = 500,
      pAdjustMethod = "BH",
      verbose = FALSE,
      seed = FALSE,
      by = "fgsea",
      geneSets = NULL
    )

### Arguments

`ind` | An interger. Index of RAV to apply GSEA.
`RAVmodel` | PCAGenomicSignature object.
`category` | A character vector representing MSigDB category. Options are "H", "C1", "C2"(default), "C3", "C4", "C5", "C6", and "C7"
`n` | An interger. The number of top and bottom enriched pathways to plot. Default is `NULL`, which prints out all the pathways enriched under `pvalueCutoff`.
`pvalueCutoff` | Cutoff for both pvalue and p.adjust. Default is 0.5.
`minGSSize` | A mininum size of gene set to be analyzed
`maxGSSize` | A maximum size of gene set to be analyzed
`pAdjustMethod` | p-value adjustment methods, which will be used as an input for `method` argument of `p.adjust` function. Available options are "holm", "hochberg", "hommel", "bonferroni", "BH"(default), "BY", "fdr", "none".
`verbose` | Logical. Default is FALSE.
`seed` | Logical. Default is FALSE.
`by` | Available options are `c("fgsea", "DOSE")`. Default "fgsea".
`geneSets` | Custom genesets to use with MSigDB genesets. It should be in a named list format.

### Value

Barplot of GSEA output. Top and bottom `n` genesets based on NES are plotted and qvalues are denoted by color.

[Package GenomicSuperSignature version 1.2.1 Index]