GOHits Class

The GOHits class extends the Hits class to represent hits that also describe relations between genes and sets using the Gene Ontology controlled vocabulary.

GOEvidenceCodes

GOOntologyCodes

GOHits(from = integer(0), to = integer(0),
  evidence = factor(character(0), names(GOEvidenceCodes)),
  ontology = factor(character(0), names(GOOntologyCodes)), nLnode = 0L,
  nRnode = 0L, ...)

Arguments

from, to	Two integer vectors of the same length. The values in `from` must be >= 1 and <= `nLnode`. The values in `to` must be >= 1 and <= `nRnode`.
evidence	factor. Levels must be values in `names(GOEvidenceCodes)`.
ontology	factor. Levels must be values in `names(GOOntologyCodes)`.
nLnode, nRnode	Number of left and right nodes.
...	Arguments metadata columns to set on the `GOHits` object. All the metadata columns must be vector-like objects of the same length as `from`, `to`, and `membership`.

Format

A named vector of length 26.

names: Code.
carat: Description.

Source

Evidence codes: http://geneontology.org/docs/guide-go-evidence-codes/

Namespaces: http://geneontology.org/docs/guide-go-evidence-codes/

Value

A GOHits object.

Details

This class does not define any additional slot to the Hits class. However, this class defines additional validity checks to ensure that every relation stored in a GOHits are respect the Gene Ontology evidence and ontology codes. Refer to GOOntologyCodes and GOEvidenceCodes for valid code and vocabulary.

Controlled vocabulary

Gene Ontology evidence codes were obtained from http://geneontology.org/docs/guide-go-evidence-codes/

Gene Ontology namespaces were obtained from http://geneontology.org/docs/ontology-documentation/

Examples

# Controlled vocabulary ----

GOEvidenceCodes
#>                                                     EXP 
#>                              "Inferred from Experiment" 
#>                                                     IDA 
#>                            "Inferred from Direct Assay" 
#>                                                     IPI 
#>                    "Inferred from Physical Interaction" 
#>                                                     IMP 
#>                        "Inferred from Mutant Phenotype" 
#>                                                     IGI 
#>                     "Inferred from Genetic Interaction" 
#>                                                     IEP 
#>                      "Inferred from Expression Pattern" 
#>                                                     HTP 
#>              "Inferred from High Throughput Experiment" 
#>                                                     HDA 
#>            "Inferred from High Throughput Direct Assay" 
#>                                                     HMP 
#>        "Inferred from High Throughput Mutant Phenotype" 
#>                                                     HGI 
#>     "Inferred from High Throughput Genetic Interaction" 
#>                                                     HEP 
#>      "Inferred from High Throughput Expression Pattern" 
#>                                                     IBA 
#>   "Inferred from Biological characteristic of Ancestor" 
#>                                                     IBD 
#> "Inferred from Biological characteristic of Descendant" 
#>                                                     IKR 
#>          "Inferred loss due to absence of Key Residues" 
#>                                                     IRD 
#>                  "Inferred loss after Rapid Divergence" 
#>                                                     ISS 
#>       "Inferred from Sequence or structural Similarity" 
#>                                                     ISO 
#>                      "Inferred from Sequence Orthology" 
#>                                                     ISA 
#>                      "Inferred from Sequence Alignment" 
#>                                                     ISM 
#>                          "Inferred from Sequence Model" 
#>                                                     IGC 
#>                         "Inferred from Genomic Context" 
#>                                                     RCA 
#>         "Inferred from Reviewed Computational Analysis" 
#>                                                     TAS 
#>                            "Traceable Author Statement" 
#>                                                     NAS 
#>                        "Non-traceable Author Statement" 
#>                                                      IC 
#>                                   "Inferred by Curator" 
#>                                                      ND 
#>                          "No biological Data available" 
#>                                                     IEA 
#>                   "Inferred from Electronic Annotation" 
GOOntologyCodes
#>                   BP                   MF                   CC 
#> "Biological Process" "Molecular Function" "Cellular Component" 

# Constructor ----

from <- c(5, 2, 3, 3, 3, 2)
to <- c(11, 15, 5, 4, 5, 11)
ontology <- factor(c("BP", "BP", "BP", "MF", "MF", "CC"))
evidence <- factor(c("IEA", "IDA", "IEA", "IDA", "IEA", "IDA"))

gh <- GOHits(from, to, evidence, ontology, 7, 15)
gh
#> GOHits object with 6 hits and 2 metadata columns:
#>            from        to | ontology evidence
#>       <integer> <integer> | <factor> <factor>
#>   [1]         5        11 |       BP      IEA
#>   [2]         2        15 |       BP      IDA
#>   [3]         3         5 |       BP      IEA
#>   [4]         3         4 |       MF      IDA
#>   [5]         3         5 |       MF      IEA
#>   [6]         2        11 |       CC      IDA
#>   -------
#>   nLnode: 7 / nRnode: 15