Description

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

Usage

data(SCOP.fa2HPMI)

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.fa2HPMI)
SCOP.fa2HPMI

An object of S4 class 'Anno'
@annoData: 58 domains, 8 terms 
@termData (InfoDataFrame)
  termNames: HP:0000006 HP:0000007 HP:0001425 ... HP:0001442 HP:0001419
    (8 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: 46463 46580 47006 ... 140830 141073 (58 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(SCOP.fa2HPMI)

An object of S4 class 'InfoDataFrame'
  rowNames: HP:0000006 HP:0000007 HP:0001425 ... HP:0001442 HP:0001419
    (8 total)
  colNames: ID Name Namespace Distance

# retrieve info on SCOP domains
domainData(SCOP.fa2HPMI)

An object of S4 class 'InfoDataFrame'
  rowNames: 46463 46580 47006 ... 140830 141073 (58 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(SCOP.fa2HPMI)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
      HP:0000006 HP:0000007 HP:0001428 HP:0010985 HP:0001417
46463          1          .          .          .          .
46580          1          .          .          .          .
47006          .          1          .          .          .
47204          .          1          .          .          .
47455          1          .          .          .          .

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

      HP:0000006 HP:0000007 HP:0001428 HP:0010985 HP:0001417
46463          1          0          0          0          0
46580          1          0          0          0          0
47006          0          1          0          0          0
47204          0          1          0          0          0
47455          1          0          0          0          0

See also