Definition for S4 class Eoutput

Description

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

Value

Class Eoutput

Slots

domainA character specifying the domain identity

ontologyA character specifying the ontology identity

term_infoA 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")

annoA 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)

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

backgroundA 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

overlapA 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)

zscoreA vector of terms, containing z-scores

pvalueA vector of terms, containing p-values

adjpA 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

Examples

# 1) load SCOP.sf (as 'InfoDataFrame' object) SCOP.sf <- dcRDataLoader('SCOP.sf')
'SCOP.sf' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment
# 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")
Start at 2015-07-23 13:17:24 First, load the ontology 'GOMF', the domain 'SCOP.sf', and their associations (2015-07-23 13:17:24) ... 'onto.GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment 'SCOP.sf' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment 'SCOP.sf2GOMF' (from package 'dcGOR' version 1.0.5) has been loaded into the working environment Second, perform enrichment analysis using HypergeoTest (2015-07-23 13:17:57) ... There are 811 terms being used, each restricted within [10,1000] annotations Last, adjust the p-values using the BH method (2015-07-23 13:17:57) ... End at 2015-07-23 13:17:57 Runtime in total is: 33 secs
eoutput
An object of S4 class 'Eoutput', containing following slots: @domain: 'SCOP.sf' @ontology: 'GOMF' @term_info: a data.frame of 52 terms X 5 information @anno: a list of 52 terms, each storing annotated domains @data: a vector containing a group of 9 input domains (annotatable) @background: a vector containing a group of 1083 background domains (annotatable) @overlap: a list of 52 terms, each containing domains overlapped with input domains @zscore: a vector of 52 terms, containing z-scores @pvalue: a vector of 52 terms, containing p-values @adjp: a vector of 52 terms, containing adjusted p-values In summary, a total of 52 terms ('GOMF') are analysed for a group of 9 input domains ('SCOP.sf')
# 3) write into the file 'Eoutput.txt' in your local directory write(eoutput, file='Eoutput.txt')
A file ('Eoutput.txt') has been written into your local directory ('/Users/hfang/Sites/SUPERFAMILY/dcGO/dcGOR')
# 4) view the top 5 significant terms view(eoutput, top_num=5, sortBy="pvalue", details=TRUE)
term_id nAnno nGroup nOverlap zscore pvalue adjp GO:0043169 GO:0043169 100 9 3 2.51 0.006 0.31 GO:0016831 GO:0016831 168 9 3 1.48 0.037 0.52 GO:0017162 GO:0017162 291 9 4 1.19 0.064 0.52 GO:0032403 GO:0032403 293 9 4 1.18 0.066 0.52 GO:0016653 GO:0016653 297 9 4 1.15 0.069 0.52 term_name GO:0043169 cation binding GO:0016831 carboxy-lyase activity GO:0017162 aryl hydrocarbon receptor binding GO:0032403 protein complex binding GO:0016653 oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor term_namespace term_distance members GO:0043169 molecular_function 3 89796,51905,47323 GO:0016831 molecular_function 4 89796,51905,47323 GO:0017162 molecular_function 4 103511,51905,47323,54631 GO:0032403 molecular_function 3 89796,51905,54631,63562 GO:0016653 molecular_function 4 103511,51905,47323,54631
# 4) retrieve several slots directly zscore(eoutput)[1:5]
GO:0004872 GO:0005215 GO:0005488 GO:0030234 GO:0060089 -0.0934 -0.2180 0.5460 -0.2700 -0.0934
pvalue(eoutput)[1:5]
GO:0004872 GO:0005215 GO:0005488 GO:0030234 GO:0060089 0.39 0.46 0.16 0.46 0.39
adjp(eoutput)[1:5]
GO:0004872 GO:0005215 GO:0005488 GO:0030234 GO:0060089 0.53 0.58 0.52 0.58 0.53

See also

Eoutput-method