factorbackground-class: Class '"factorbackground"'

In AtlasRDF: Gene Expression Atlas query and gene set enrichment package.

Description

Used in enrichment to represent an experimental factor and any associated genes for that factor as well as additional ontological information about the factor.

Extends

All reference classes extend and inherit methods from "envRefClass".

Fields

uri:

Object of class character URI of the experimental factor.

label:

Object of class character name of the experimental factor.

species:

Object of class character Species ID of the experimental factor.

geneuris:

Object of class vector URIs of the genes for this experimental factor.

numgenesexpressed:

Object of class integer Count of the genes expressed for this factor.

numgenesnotexpressed:

Object of class integer Count of the genes not expressed for this factor from the total genes for this species.

subclasses:

Object of class vector Subclass of this factor from ontology

superclasses:

Object of class vector Superclasses of this factor from ontology

Methods

mergegeneuris(value):

Merge gene URIs into the current vector

getsuperclasses():

Get superclasses for this factor from the ontology

setsuperclasses(value):

Set superclasses for this factor from the ontology

getsubclasses():

Get subclasses for this factor from the ontology

setsubclasses(value):

Set ontology subclasses for this factor

getnumgenesnotexpressed():

Get the number of genes not expressed for this factor as a total from total number of genes for this species

setnumgenesnotexpressed(value):

Set the number of genes not expressed for this factor as a total from total number of genes for this species

getnumgenesexpressed():

Get the number of genes expressed for this factor.

setnumgenesexpressed(value):

Set the number of genes expressed for this factor.

getgeneuris():

Get URIs for genes differentially expressed for this factor.

setgeneuris(value):

Set URIs for genes differentially expressed for this factor.

getspecies():

Get species ID for this factor.

setspecies(value):

Set species ID for this factor.

getlabel():

Get name for this factor.

setlabel(value):

Set name for this factor.

geturi():

Get the URI for this factor.

seturi(value):

Set the URI for this factor.

Author(s)

James Malone, Simon Jupp

Examples

showClass("factorbackground")

AtlasRDF documentation built on Nov. 17, 2017, 9:33 a.m.