EnrichAB {MAGeCKFlute} | R Documentation

## Enrichment analysis for Positive and Negative selection genes

### Description

Do enrichment analysis for selected genes, in which positive selection and negative selection are termed as GroupA and GroupB

### Usage

    EnrichAB(
      data,
      pvalue = 0.25,
      enrich_method = "ORT",
      organism = "hsa",
      limit = c(1, 120),
      filename = NULL,
      out.dir = ".",
      width = 6.5,
      height = 4,
      verbose = TRUE,
      ...
    )

### Arguments

`data` | A data frame.
`pvalue` | Pvalue cutoff.
`enrich_method` | One of "ORT"(Over-Representing Test) and "HGT"(HyperGemetric test).
`organism` | "hsa" or "mmu".
`limit` | A two-length vector (default: c(1, 120)), specifying the min and max size of pathways for enrichent analysis.
`filename` | Suffix of output file name.
`out.dir` | Path to save plot to (combined with filename).
`width` | As in ggsave.
`height` | As in ggsave.
`verbose` | Boolean
`...` | Other available parameters in ggsave.

### Value

A list containing enrichment results for each group genes. This list contains eight items, which contain subitems of `gridPlot` and `enrichRes`.

### Author(s)

Wubing Zhang

[Package MAGeCKFlute version 1.12.0 Index]