Eoutput is an S4 class to store output from enrichment analysis
by dcEnrichment.
Class Eoutput
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
An object of this class can be created via: new("Eoutput",
domain, ontology, term_info, anno, data, overlap, zscore, pvalue,
adjp)
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
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
# 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 secseoutputAn 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 -0.0934pvalue(eoutput)[1:5]GO:0004872 GO:0005215 GO:0005488 GO:0030234 GO:0060089 0.39 0.46 0.16 0.46 0.39adjp(eoutput)[1:5]GO:0004872 GO:0005215 GO:0005488 GO:0030234 GO:0060089 0.53 0.58 0.52 0.58 0.53
Eoutput-method