MeSHHyperGResult-class {meshr} | R Documentation

## Class "MeSHHyperGResult"

### Description

This class represents the results of a test for overrepresentation of MeSH terms among genes in a selected gene set based upon the Hypergeometric distribution.

For details on extracting information from this object, please read the documentation in the MeSHHyperGParams-class.

### Objects from the Class

Objects can be created by calls of the form `new("MeSHHyperGResult", ...)`.

### Slots

`meshCategory`:

  Object of class `"character"` representing the category of MeSH terms tested.

`meshAnnotation`:

  Object of class `"character"`. The name of the annotation data used in the analysis.

`meshDatabase`:

  Object of class `"character"`. The name of the database used in the analysis.

`ORA`:

  Object of class `"data.frame"`. MeSH IDs, MeSH Terms, P-value, and other statistics is returned.

### Methods

meshCategory

  `signature(r = "MeSHHyperGResult")`: Returns the MeSH category used in the analysis.

meshAnnotation

  `signature(r = "MeSHHyperGResult")`: Returns the name of the annotation data used in the analysis.

meshDatabase

  `signature(r = "MeSHHyperGResult")`: Returns the name of the database used in the analysis.

meshIds

  `signature(r = "MeSHHyperGResult")`: Returns the character vector of the MeSH IDs identified as significant in the analysis.

meshTerms

  `signature(r = "MeSHHyperGResult")`: Returns the character vector of the MeSH terms identified as significant in the analysis.

pvalues

  `signature(r = "MeSHHyperGResult")`: Returns the associated p-values of significantly enriched MeSH terms.

summary

  `signature(r = "MeSHHyperGResult")`: Returns a `data.frame` summarizing the test result. Optional arguments `pvalue` and `categorySize` allow specification of maximum p-value and minimum categorySize, respectively. Optional argument `htmlLinks` is a logical value indicating whether to add HTML links (useful in conjunction with xtables print method with `type` set to `"html"`).

show

  `signature(object = "MeSHHyperGResult")`: Return a short description of the result.

save.pdf

  `signature(object = "MeSHHyperGResult")`: Return PDF files corresponding PMCID. This function is available only when using gene2pubmed as database

### Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>

### See Also

`meshr-package`, `MeSHHyperGParams-class`, `meshHyperGTest`

[Package meshr version 1.15.0 Index]