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", pathway_limit = c(3, 50), adjust = "BH",
      filename = NULL, out.dir = ".", gsea = FALSE, width = 6.5,
      height = 4, ...)

### Arguments

`data` | A data frame containing columns "diff", with rownames of Entrez IDs.
`pvalue` | Pvalue cutoff.
`enrich_method` | One of "ORT"(Over-Representing Test), "GSEA"(Gene Set Enrichment Analysis), and "HGT"(HyperGemetric test).
`organism` | "hsa" or "mmu".
`pathway_limit` | A two-length vector (default: c(3, 50)), specifying the min and max size of pathways for enrichent analysis.
`adjust` | One of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", and "none".
`filename` | Suffix of output file name.
`out.dir` | Path to save plot to (combined with filename).
`gsea` | Boolean, specifying if do GSEA for GroupA and GroupB genes. Default gsea = FALSE.
`width` | As in ggsave.
`height` | As in ggsave.
`...` | Other available parameters in ggsave.

### Value

A list containing enrichment results for each group genes. This list contains items four items, `keggA`, `keggB`, `goA`, `goB`. Four items are all list object, containing subitems of `gridPlot` and `enrichRes`. `gridPlot` is a ggplot object, and `enrichRes` is a enrichResult instance

### Author(s)

Binbin Wang

### See Also

`EnrichSquare`

### Examples

    data(mle.gene_summary)
    # Read beta score from gene summary table in MAGeCK MLE results
    dd = ReadBeta(mle.gene_summary, organism="hsa")
    data=ScatterView(dd, ctrlname = "dmso", treatname = "plx")$data
    ## Not run:
      #GO and KEGG enrichment analysis
     enrich_result = EnrichAB(data, pvalue=0.05, organism="hsa")
      print(enrich_result$keggA$gridPlot)
      print(enrich_result$goA$gridPlot)

    ## End(Not run)

[Package MAGeCKFlute version 1.2.3 Index]