Description

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

Usage

data(SCOP.sf2GOBP)

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.sf2GOBP)
SCOP.sf2GOBP

An object of S4 class 'Anno'
@annoData: 1163 domains, 9058 terms 
@termData (InfoDataFrame)
  termNames: GO:0008150 GO:0000003 GO:0001906 ... GO:0061470 GO:0072540
    (9058 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: 46458 46548 46561 ... 161111 161256 (1163 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(SCOP.sf2GOBP)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0008150 GO:0000003 GO:0001906 ... GO:0061470 GO:0072540
    (9058 total)
  colNames: ID Name Namespace Distance

# retrieve info on SCOP domains
domainData(SCOP.sf2GOBP)

An object of S4 class 'InfoDataFrame'
  rowNames: 46458 46548 46561 ... 161111 161256 (1163 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.sf2GOBP)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
      GO:0009265 GO:0000003 GO:0009266 GO:0050817 GO:0043268
46458          .          .          .          1          .
46548          .          .          .          .          .
46561          .          .          .          .          .
46565          .          .          1          .          .
46579          .          .          .          .          .

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

      GO:0009265 GO:0000003 GO:0009266 GO:0050817 GO:0043268
46458          0          0          0          1          0
46548          0          0          0          0          0
46561          0          0          0          0          0
46565          0          0          1          0          0
46579          0          0          0          0          0

See also