Pfam2GOBP: Annotations of Pfam domains by Gene Ontology Biological...

In dcGOR: Analysis of Ontologies and Protein Domain Annotations

Description

An object of class "Anno" that contains associations between Gene Ontology Biological Process terms and Pfam domains. This data is prepared based on the Pfam database (see http://pfam.xfam.org) and ftp://ftp.geneontology.org/pub/go/external2go/pfam2go.

Usage

data(Pfam2GOBP)

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 Pfam accession ID, and "level" always equals "Pfam", "description" for Pfam description

References

Finn et al. (2014) The Pfam protein families database. Nucleic Acids Res, 42(Database issue):D222-D230.

See Also

Anno-class

Examples

# load data
data(Pfam2GOBP)
Pfam2GOBP
# retrieve info on ontology terms
termData(Pfam2GOBP)
# retrieve info on Pfam domains
domainData(Pfam2GOBP)
# retrieve the first 5 rows and columns of annotation data
x <- annoData(Pfam2GOBP)[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: 3241 domains, 1005 terms 
@termData (InfoDataFrame)
  termNames: GO:0008152 GO:0040007 GO:0048511 ... GO:0019281 GO:0032862
    (1005 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: PF00001 PF00002 PF00003 ... PF15550 PF15556 (3241 total)
  dvarLabels: id level description
An object of S4 class 'InfoDataFrame'
  rowNames: GO:0008152 GO:0040007 GO:0048511 ... GO:0019281 GO:0032862
    (1005 total)
  colNames: ID Name Namespace Distance
An object of S4 class 'InfoDataFrame'
  rowNames: PF00001 PF00002 PF00003 ... PF15550 PF15556 (3241 total)
  colNames: id level description
5 x 5 sparse Matrix of class "dgCMatrix"
        GO:0006635 GO:0030639 GO:0030682 GO:0016255 GO:0006650
PF00001          .          .          .          .          .
PF00002          .          .          .          .          .
PF00003          .          .          .          .          .
PF00015          .          .          .          .          .
PF00026          .          .          .          .          .
        GO:0006635 GO:0030639 GO:0030682 GO:0016255 GO:0006650
PF00001          0          0          0          0          0
PF00002          0          0          0          0          0
PF00003          0          0          0          0          0
PF00015          0          0          0          0          0
PF00026          0          0          0          0          0

dcGOR documentation built on May 2, 2019, 3:34 p.m.