Eoutput-class: Definition for S4 class Eoutput

In hfang-bristol/dcGOR: Analysis of Ontologies and Protein Domain Annotations

Definition for S4 class Eoutput

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)

hfang-bristol/dcGOR documentation built on July 16, 2022, 6:43 p.m.