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.

Examples

# load data
data(Pfam2GOBP)
Pfam2GOBP

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

# retrieve info on ontology terms
termData(Pfam2GOBP)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0008152 GO:0040007 GO:0048511 ... GO:0019281 GO:0032862
    (1005 total)
  colNames: ID Name Namespace Distance

# retrieve info on Pfam domains
domainData(Pfam2GOBP)

An object of S4 class 'InfoDataFrame'
  rowNames: PF00001 PF00002 PF00003 ... PF15550 PF15556 (3241 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(Pfam2GOBP)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
        GO:0006635 GO:0030639 GO:0030682 GO:0016255 GO:0006650
PF00001          .          .          .          .          .
PF00002          .          .          .          .          .
PF00003          .          .          .          .          .
PF00015          .          .          .          .          .
PF00026          .          .          .          .          .

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

        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

See also