Description

An object of class "Anno" that contains associations between Gene Ontology Cellular Component terms and InterPro domains. This data is prepared based on the InterPro database (see http://www.ebi.ac.uk/interpro/) and ftp://anonymous@ftp.ebi.ac.uk/pub/databases/interpro/Current/interpro2go.

Usage

data(InterPro2GOCC)

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 InterPro ID, and "level" always equals "InterPro", "description" for InterPro description

References

Hunter et al. (2012) Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. Database (Oxford), 2012:bar068.

Examples

# load data
data(InterPro2GOCC)
InterPro2GOCC

An object of S4 class 'Anno'
@annoData: 4961 domains, 488 terms 
@termData (InfoDataFrame)
  termNames: GO:0005576 GO:0009295 GO:0016020 ... GO:0042729 GO:0044196
    (488 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: IPR000003 IPR000009 IPR000012 ... IPR029781 IPR029782
    (4961 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(InterPro2GOCC)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0005576 GO:0009295 GO:0016020 ... GO:0042729 GO:0044196
    (488 total)
  colNames: ID Name Namespace Distance

# retrieve info on InterPro domains
domainData(InterPro2GOCC)

An object of S4 class 'InfoDataFrame'
  rowNames: IPR000003 IPR000009 IPR000012 ... IPR029781 IPR029782 (4961
    total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(InterPro2GOCC)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
          GO:0000220 GO:0000221 GO:0045281 GO:0000228 GO:0072546
IPR000003          .          .          .          .          .
IPR000009          .          .          .          .          .
IPR000012          .          .          .          .          .
IPR000013          .          .          .          .          .
IPR000015          .          .          .          .          .

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

          GO:0000220 GO:0000221 GO:0045281 GO:0000228 GO:0072546
IPR000003          0          0          0          0          0
IPR000009          0          0          0          0          0
IPR000012          0          0          0          0          0
IPR000013          0          0          0          0          0
IPR000015          0          0          0          0          0

See also