Eoutput-class: Definition for S4 class Eoutput

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description

Eoutput is an S4 class to store output from enrichment analysis by dcEnrichment.

Value

Class Eoutput

Slots

domain

A character specifying the domain identity

ontology

A character specifying the ontology identity

term_info

A data.frame of nTerm X 5 containing term information, where nTerm is the number of terms in consideration, and the 5 columns are "term_id" (i.e. "Term ID"), "term_name" (i.e. "Term Name"), "namespace" (i.e. "Term Namespace"), "distance" (i.e. "Term Distance") and "IC" (i.e. "Information Content for the term based on annotation frequency by it")

anno

A list of terms, each storing annotated domains (also within the background domains). Always, terms are identified by "term_id" and domain members identified by their ids (e.g. sunids for SCOP domains)

data

A vector containing input data in dcEnrichment. It is not always the same as the input data as only those mappable are retained

background

A vector containing background in dcEnrichment. It is not always the same as the input background (if provided by the user) as only those mappable are retained

overlap

A list of terms, each storing domains overlapped between domains annotated by a term and domains in the input data (i.e. the domains of interest). Always, terms are identified by "term_id" and domain members identified by their ids (e.g. sunids for SCOP domains)

zscore

A vector of terms, containing z-scores

pvalue

A vector of terms, containing p-values

adjp

A vector of terms, containing adjusted p-values. It is the p value but after being adjusted for multiple comparisons

Creation

An object of this class can be created via: new("Eoutput", domain, ontology, term_info, anno, data, overlap, zscore, pvalue, adjp)

Methods

Class-specific methods:

• zscore(): retrieve the slot 'zscore' in the object

• pvalue(): retrieve the slot 'pvalue' in the object

• adjp(): retrieve the slot 'adjp' in the object

• view(): retrieve an integrated data.frame used for viewing the object

• write(): write the object into a local file

Standard generic methods:

• str(): compact display of the content in the object

• show(): abbreviated display of the object

Access

Ways to access information on this class:

• showClass("Eoutput"): show the class definition

• showMethods(classes="Eoutput"): show the method definition upon this class

• getSlots("Eoutput"): get the name and class of each slot in this class

• slotNames("Eoutput"): get the name of each slot in this class

• selectMethod(f, signature="Eoutput"): retrieve the definition code for the method 'f' defined in this class

See Also

Eoutput-method

Examples

## Not run: 
# 1) load SCOP.sf (as 'InfoDataFrame' object)
SCOP.sf <- dcRDataLoader('SCOP.sf')
# randomly select 20 domains
data <- sample(rowNames(SCOP.sf), 20)

# 2) perform enrichment analysis, producing an object of S4 class 'Eoutput'
eoutput <- dcEnrichment(data, domain="SCOP.sf", ontology="GOMF")
eoutput

# 3) write into the file 'Eoutput.txt' in your local directory
write(eoutput, file='Eoutput.txt')

# 4) view the top 5 significant terms
view(eoutput, top_num=5, sortBy="pvalue", details=TRUE)

# 4) retrieve several slots directly
zscore(eoutput)[1:5]
pvalue(eoutput)[1:5]
adjp(eoutput)[1:5]

## End(Not run)

dcGOR documentation built on May 2, 2019, 6:14 p.m.