Description

An object of class "Anno" that contains associations between Gene Ontology Cellular Component terms and Rfam RNA families. This data is prepared based on the Rfam database (see http://rfam.xfam.org) and http://geneontology.org/external2go/rfam2go.

Usage

data(Rfam2GOCC)

Value

an object of class Anno. It has slots for "annoData", "termData" and "domainData":

• annoData: a sparse matrix of RNAs 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 RNAs (i.e. rows in annoData), including: "id" for Rfam accession ID, and "level" always equals "Rfam", "description" for Rfam description

References

Gardner et al. (2011) Rfam: Wikipedia, clans and the "decimal" release. Nucleic Acids Res, 39(Database issue):D141-D145.

Examples

# load data
data(Rfam2GOCC)
Rfam2GOCC

An object of S4 class 'Anno'
@annoData: 1232 domains, 25 terms 
@termData (InfoDataFrame)
  termNames: GO:0005737 GO:0005840 GO:0030677 ... GO:0016607 GO:0042382
    (25 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: RF00001 RF00002 RF00003 ... RF02245 RF02254 (1232 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(Rfam2GOCC)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0005737 GO:0005840 GO:0030677 ... GO:0016607 GO:0042382
    (25 total)
  colNames: ID Name Namespace Distance

# retrieve info on Rfam RNAs
domainData(Rfam2GOCC)

An object of S4 class 'InfoDataFrame'
  rowNames: RF00001 RF00002 RF00003 ... RF02245 RF02254 (1232 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(Rfam2GOCC)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
        GO:0005685 GO:0005693 GO:0005686 GO:0005730 GO:0005737
RF00001          .          .          .          .          .
RF00002          .          .          .          .          .
RF00003          1          .          .          .          .
RF00004          .          .          1          .          .
RF00007          .          1          .          .          .

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

        GO:0005685 GO:0005693 GO:0005686 GO:0005730 GO:0005737
RF00001          0          0          0          0          0
RF00002          0          0          0          0          0
RF00003          1          0          0          0          0
RF00004          0          0          1          0          0
RF00007          0          1          0          0          0

See also