Description

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

Usage

data(SCOP.fa2MP)

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.fa2MP)
SCOP.fa2MP

An object of S4 class 'Anno'
@annoData: 364 domains, 2139 terms 
@termData (InfoDataFrame)
  termNames: MP:0001186 MP:0002006 MP:0002873 ... MP:0009922 MP:0009926
    (2139 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: 46690 46739 46748 ... 161112 161211 (364 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(SCOP.fa2MP)

An object of S4 class 'InfoDataFrame'
  rowNames: MP:0001186 MP:0002006 MP:0002873 ... MP:0009922 MP:0009926
    (2139 total)
  colNames: ID Name Namespace Distance

# retrieve info on SCOP domains
domainData(SCOP.fa2MP)

An object of S4 class 'InfoDataFrame'
  rowNames: 46690 46739 46748 ... 161112 161211 (364 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2MP)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
      MP:0000159 MP:0003564 MP:0001697 MP:0000440 MP:0001698
46690          .          .          .          .          .
46739          .          .          .          .          .
46748          .          .          .          .          .
46775          .          .          .          .          .
46827          .          .          .          .          .

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

      MP:0000159 MP:0003564 MP:0001697 MP:0000440 MP:0001698
46690          0          0          0          0          0
46739          0          0          0          0          0
46748          0          0          0          0          0
46775          0          0          0          0          0
46827          0          0          0          0          0

See also