Description

An object of class "Anno" that contains associations between Gene Ontology Molecular Function 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(Rfam2GOMF)

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(Rfam2GOMF)
Rfam2GOMF

An object of S4 class 'Anno'
@annoData: 93 domains, 23 terms 
@termData (InfoDataFrame)
  termNames: GO:0003824 GO:0003735 GO:0005515 ... GO:0003720 GO:0004526
    (23 total)
  tvarLabels: ID Name Namespace Distance
@domainData (InfoDataFrame)
  domainNames: RF00001 RF00002 RF00003 ... RF02276 RF02277 (93 total)
  dvarLabels: id level description

# retrieve info on ontology terms
termData(Rfam2GOMF)

An object of S4 class 'InfoDataFrame'
  rowNames: GO:0003824 GO:0003735 GO:0005515 ... GO:0003720 GO:0004526
    (23 total)
  colNames: ID Name Namespace Distance

# retrieve info on Rfam RNAs
domainData(Rfam2GOMF)

An object of S4 class 'InfoDataFrame'
  rowNames: RF00001 RF00002 RF00003 ... RF02276 RF02277 (93 total)
  colNames: id level description

# retrieve the first 5 rows and columns of annotation data
x <- annoData(Rfam2GOMF)[1:5,1:5]
x

5 x 5 sparse Matrix of class "dgCMatrix"
        GO:0030533 GO:0030622 GO:0045131 GO:0030621 GO:0000171
RF00001          .          .          .          .          .
RF00002          .          .          .          .          .
RF00003          .          .          .          .          .
RF00004          .          .          1          .          .
RF00005          1          .          .          .          .

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

        GO:0030533 GO:0030622 GO:0045131 GO:0030621 GO:0000171
RF00001          0          0          0          0          0
RF00002          0          0          0          0          0
RF00003          0          0          0          0          0
RF00004          0          0          1          0          0
RF00005          1          0          0          0          0

See also