Description

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

Usage

SCOP.fa2UP <- dcRDataLoader(RData = "SCOP.fa2UP")

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
SCOP.fa2UP <- dcRDataLoader(RData='SCOP.fa2UP')

'SCOP.fa2UP' (from http://dcgor.r-forge.r-project.org/data/SCOP.fa2UP.RData) has been loaded into the working environment
SCOP.fa2UP

An object of S4 class 'Anno'
@annoData: 810 domains, 640 terms 
@termData (InfoDataFrame)
  termNames: UPA00026 UPA00485 UPA00942 ... UPA00901 UPA00902 (640
    total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: 46549 46553 46566 ... 160984 161211 (810 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(SCOP.fa2UP)

An object of S4 class 'InfoDataFrame'
  rowNames: UPA00026 UPA00485 UPA00942 ... UPA00901 UPA00902 (640
    total)
  colNames: ID Name Namespace Distance

# retrieve info on SCOP domains
domainData(SCOP.fa2UP)

An object of S4 class 'InfoDataFrame'
  rowNames: 46549 46553 46566 ... 160984 161211 (810 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2UP)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
      UPA00458 UPA00199 UPA00201 UPA00460 UPA00202
46549        .        .        .        .        .
46553        .        .        1        .        .
46566        .        .        .        1        .
46590        .        .        .        .        .
46685        .        .        .        .        .

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

      UPA00458 UPA00199 UPA00201 UPA00460 UPA00202
46549        0        0        0        0        0
46553        0        0        1        0        0
46566        0        0        0        1        0
46590        0        0        0        0        0
46685        0        0        0        0        0

See also