EnrichSquare {MAGeCKFlute} | R Documentation

## Enrichment analysis for selected treatment related genes

### Description

Do enrichment analysis for selected treatment related genes in 9-squares

### Usage

    EnrichSquare(beta, pvalue = 0.05, enrich_method = "ORT",
      organism = "hsa", pathway_limit = c(3, 50), adjust = "BH",
      filename = NULL, out.dir = ".", width = 6.5, height = 4, ...)

### Arguments

`beta` | Data frame, with rownames of Entrez IDs, which contains columns of 'group' and 'diff'.
`pvalue` | Pvalue cutoff.
`enrich_method` | One of "ORT"(Over-Representing Test) 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", "none".
`filename` | Suffix of output file name. NULL(default) means no output.
`out.dir` | Path to save plot to (combined with filename).
`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 several elements:

`kegg1` | a list record enriched KEGG pathways for Group1 genes in 9-Square
`kegg2` | a list record enriched KEGG pathways for Group2 genes in 9-Square
`kegg3` | a list record enriched KEGG pathways for Group3 genes in 9-Square
`kegg4` | a list record enriched KEGG pathways for Group4 genes in 9-Square
`kegg13` | a list record enriched KEGG pathways for Group1&Group3 genes in 9-Square
`kegg14` | a list record enriched KEGG pathways for Group1&Group4 genes in 9-Square
`kegg23` | a list record enriched KEGG pathways for Group2&Group3 genes in 9-Square
`kegg24` | a list record enriched KEGG pathways for Group2&Group4 genes in 9-Square
`go1` | a list record enriched GO terms for Group1 genes in 9-Square
`go2` | a list record enriched GO terms for Group2 genes in 9-Square
`go3` | a list record enriched GO terms for Group3 genes in 9-Square
`go4` | a list record enriched GO terms for Group4 genes in 9-Square
`go13` | a list record enriched GO terms for Group1&Group3 genes in 9-Square
`go14` | a list record enriched GO terms for Group1&Group4 genes in 9-Square
`go23` | a list record enriched GO terms for Group2&Group3 genes in 9-Square
`go24` | a list record enriched GO terms for Group2&Group4 genes in 9-Square

Each item in the returned list has two sub items:

`gridPlot` | an object created by `ggplot`, which can be assigned and further customized.
`enrichRes` | a enrichResult instance.

### Author(s)

Wubing Zhang

### See Also

`SquareView`

`EnrichSquare`

### Examples

    data(mle.gene_summary)
    dd = ReadBeta(mle.gene_summary, organism="hsa")
    p = SquareView(dd, ctrlname = "dmso", treatname = "plx")
    ## Not run:
     # Read beta score from gene summary table in MAGeCK MLE results
     E1 = EnrichSquare(p$data, organism="hsa")
     print(E1$kegg1$gridPlot)

    ## End(Not run)

[Package MAGeCKFlute version 1.2.3 Index]