MeSHHyperGResult-class: Class "MeSHHyperGResult"

Description Objects from the Class Slots Methods Author(s) See Also

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 <[email protected]>

See Also

meshr-package, MeSHHyperGParams-class, meshHyperGTest


meshr documentation built on May 6, 2019, 2:23 a.m.