InterPro2GOMF: Annotations of InterPro domains by Gene Ontology Molecular...

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description

An object of class "Anno" that contains associations between Gene Ontology Molecular Function terms and InterPro domains. This data is prepared based on the InterPro database (see http://www.ebi.ac.uk/interpro/) and ftp://[e-mail]/pub/databases/interpro/Current/interpro2go.

Usage

data(InterPro2GOMF)

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.

See Also

Anno-class

Examples

# load data
data(InterPro2GOMF)
InterPro2GOMF
# retrieve info on ontology terms
termData(InterPro2GOMF)
# retrieve info on InterPro domains
domainData(InterPro2GOMF)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(InterPro2GOMF)[1:5,1:5]
x
# convert the above retrieval to the full matrix
as.matrix(x)

Example output

Loading required package: Matrix
Loading required package: igraph

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

Loading required package: dnet
Loading required package: supraHex
Loading required package: hexbin

Attaching package: ‘dcGOR’

The following object is masked from ‘package:base’:

    write

An object of S4 class 'Anno'
@annoData: 8899 domains, 2219 terms 
@termData (InfoDataFrame)
  termNames: GO:0001071 GO:0003824 GO:0004872 ... GO:0015467 GO:0072345
    (2219 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: IPR000003 IPR000006 IPR000008 ... IPR029784 IPR029785
    (8899 total)
  dvarLabels: id level description
An object of S4 class 'InfoDataFrame'
  rowNames: GO:0001071 GO:0003824 GO:0004872 ... GO:0015467 GO:0072345
    (2219 total)
  colNames: ID Name Namespace Distance
An object of S4 class 'InfoDataFrame'
  rowNames: IPR000003 IPR000006 IPR000008 ... IPR029784 IPR029785 (8899
    total)
  colNames: id level description
5 x 5 sparse Matrix of class "dgCMatrix"
          GO:0004854 GO:0003730 GO:0004855 GO:0004176 GO:0004177
IPR000003          .          .          .          .          .
IPR000006          .          .          .          .          .
IPR000008          .          .          .          .          .
IPR000009          .          .          .          .          .
IPR000010          .          .          .          .          .
          GO:0004854 GO:0003730 GO:0004855 GO:0004176 GO:0004177
IPR000003          0          0          0          0          0
IPR000006          0          0          0          0          0
IPR000008          0          0          0          0          0
IPR000009          0          0          0          0          0
IPR000010          0          0          0          0          0

dcGOR documentation built on May 2, 2019, 6:14 p.m.