Description

An object of class "Anno" that contains associations between Gene Ontology Molecular Function terms and SCOP domain families (fa). This data is prepared based on the dcGO database (see http://supfam.org/SUPERFAMILY/dcGO/).

Usage

data(SCOP.fa2GOMF)

Value

an object of class Anno. It has slots for "annoData", "termData" and "domainData":

• annoData: a sparse matrix of domains X terms
• termData: variables describing ontology terms (i.e. columns in annoData), including: "ID" (i.e. term ID), "Name" (i.e. term Names), "Namespace" (i.e. term Namespace), and "Distance" (i.e. term Distance to the ontology root)
• domainData: variables describing domains (i.e. rows in annoData), including: "id" for SCOP sunid, and "level" for SCOP level, "description" for SCOP description

References

Fang H and Gough J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Res, 41(Database issue):D536-44.

Examples

# load data
data(SCOP.fa2GOMF)
SCOP.fa2GOMF

An object of S4 class 'Anno'
@annoData: 1752 domains, 2238 terms 
@termData (InfoDataFrame)
  termNames: GO:0003674 GO:0000988 GO:0001071 ... GO:0015662 GO:0044769
    (2238 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: 46463 46549 46553 ... 161230 161235 (1752 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(SCOP.fa2GOMF)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0003674 GO:0000988 GO:0001071 ... GO:0015662 GO:0044769
    (2238 total)
  colNames: ID Name Namespace Distance

# retrieve info on SCOP domains
domainData(SCOP.fa2GOMF)

An object of S4 class 'InfoDataFrame'
  rowNames: 46463 46549 46553 ... 161230 161235 (1752 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2GOMF)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
      GO:0045703 GO:0008327 GO:0003726 GO:0008329 GO:0004497
46463          .          .          .          .          .
46549          .          .          .          .          .
46553          .          .          .          .          .
46562          .          .          .          .          .
46566          .          .          .          .          .

# convert the above retrieval to the full matrix
as.matrix(x)

      GO:0045703 GO:0008327 GO:0003726 GO:0008329 GO:0004497
46463          0          0          0          0          0
46549          0          0          0          0          0
46553          0          0          0          0          0
46562          0          0          0          0          0
46566          0          0          0          0          0

See also