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>