GOHits-class: GOHits Class

In kevinrue/unisets: Collection of Classes to Store Gene Sets

Description

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

Usage

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.

...

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.

Value

A GOHits object.

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/

Author(s)

Kevin Rue-Albrecht

Source

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

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

See Also

Hits, FuzzySets

Examples

# Controlled vocabulary ----

GOEvidenceCodes
GOOntologyCodes

# 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

kevinrue/unisets documentation built on May 15, 2020, 10:48 p.m.