dcGOR (version 1.0.2)

Eoutput-class: Definition for S4 class Eoutput

Description

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

Value

• Class Eoutput

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}

itemize

• str():

item

show():

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

# 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]