Package 'meshr'

Title: Tools for conducting enrichment analysis of MeSH
Description: A set of annotation maps describing the entire MeSH assembled using data from MeSH.
Authors: Koki Tsuyuzaki, Itoshi Nikaido, Gota Morota
Maintainer: Koki Tsuyuzaki <[email protected]>
License: Artistic-2.0
Version: 2.13.0
Built: 2024-10-30 08:43:04 UTC
Source: https://github.com/bioc/meshr

Help Index

Enrichment analysis for MeSH terms.

Description

meshr package conducts a MeSH enrichment analysis employing gene-MeSH annotation data. A hypergeometric test accounting for a multiple tesing correction is used to find significantly enriched MeSH terms.

Details

Package: meshr
Version: 1.2.6
Date: 3-20-2015
biocViews: AnnotationData, FunctionalAnnotation, Bioinformatics, Statistics, Annotation, MultipleComparisons
Depends: R (>= 3.0.1), cummeRbund, org.Hs.eg.db, fdrtool, Category, BiocGenerics, methods, MeSH.db, MeSH.AOR.db, MeSH.PCR.db, MeSHDbi, MeSH.Hsa.eg.db, MeSH.Aca.eg.db, MeSH.Atu.K84.eg.db, MeSH.Bsu.168.eg.db, MeSH.Syn.eg.db
Imports:
Suggests:
License: Artistic-2.0

Index: 

meshHyperGTest performs a hypergeometric statistical test.

Further information is available in the vignettes.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <[email protected]>

See Also

MeSHHyperGParams-class, MeSHHyperGResult-class, meshHyperGTest

Examples

ls("package:meshr")

A function to return the name of MeSH category

Description

This function returns the name of MeSH category.

Usage

category(r)
category(r) <- value

Arguments

r

An object containing annotation information.

value

The annotation information to set on object.

Author(s)

Koki Tsuyuzaki

Examples

showMethods("category")

A function to return the name of MeSH database

Description

This function returns the name of MeSH database.

Usage

database(r)
database(r) <- value

Arguments

r

An object containing annotation information.

value

The annotation information to set on object.

Author(s)

Koki Tsuyuzaki

Examples

showMethods("database")

Class "MeSHHyperGParams"

Description

A parameter class for representing all parameters needed for running the 'meshHyperGTest' method with one of the MeSH categories ("Anatomy", "Organisms", "Diseases", "Chemicals and Drugs", "Analytical, Diagnostic and Therapeutic Techniques and Equipment", "Psychiatry and Psychology", "Phenomena and Processes", "Disciplines and Occupations", "Anthropology, Education, Sociology and Social Phenomena", "Technology and Food and Beverages", "Humanities", "Information Science", "Persons", "Health Care", "Publication Type", "Geographical Locations").

Objects from the Class

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

Slots

geneIds:

Object of class "ANY": A vector of gene identifiers. Numeric and character vectors are probably the only things that make sense. These are the gene ids for the selected gene set.

universeGeneIds:

Object of class "ANY": A vector of gene ids in the same format as geneIds defining a subset of the gene ids on the chip that will be used as the universe for the hypergeometric calculation.

annotation:

A string giving the name of the gene-MeSH annotation package like MeSH.XXX.eg.db.

meshdb:

A string giving the name of the MeSH database like MeSH.db.

category:

A string giving the name of the MeSH category like A, B, C, D, ...and so on.

database:

A string giving the name of the MeSH database like gendoo, gene2pubmed, ...and so on.

pvalueCutoff:

A numeric values between zero and one used as a p-value or FDR cutoff for hypergeometric test depending on pAdjust. The default is set to 0.05.

pAdjust:

A string which can be one of the Benjamini-Hochberg procedure (a.k.a. q-value) ("BH"), Q-value ("QV"), empirical Bayes method ("lFDR"), and unadjusted p-value ("none") for multiple testing correction.

Methods

geneIds(p), geneIds(p) <- value

Accessor methods for the geneIds.

universeGeneIds(p), universeGeneIds(p) <- value

Accessor methods for the geneIds.

annotation(p), annotation(p) <- value

Accessor methods for the gene-MeSH annotation data.

pAdjust(p)

An accessor method for the choice of a method for multiple testing correction.

pvalueCutoff(p)

An accessor method for the choice of a threshold when conducting enrichment analysis.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <[email protected]>

See Also

meshr-package, MeSHHyperGResult-class, meshHyperGTest, category, database

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.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <[email protected]>

See Also

meshr-package, MeSHHyperGParams-class, meshHyperGTest

Hypergeometric Tests for MeSH term association

Description

Given a MeSHHyperGParams object containing a set of selected and background gene IDs, and gene-MeSH annotation data of interest, meshHyperGTest performs Hypergeomtric test for over-representation of each MeSH term accouting for the multiple testing correction.

Arguments

p

A MeSHHyperGParams object

Details

For details on creating MeSHHyperGParams object, please read the documentation in the MeSHHyperGParams-class.

Value

A MeSHHyperGResult object.

Author(s)

Gota Morota, Koki Tsuyuzaki, Takeru Nakazato, Itoshi Nikaido

Maintainer: Koki Tsuyuzaki <[email protected]>

See Also

meshr-package, MeSHHyperGParams-class, MeSHHyperGResult-class

Examples

showMethods("meshHyperGTest")