simLL {GOstats}R Documentation

Functions to compute similarities between GO graphs and also between LocusLink IDs based on their induced GO graphs.

Description

Both simUI and simLP compute a similarity measure between two GO graphs. For simLL, first the induced GO graph for each of its arguments is found and then these are passed to one of simUI or simLP.

Usage

simLL(ll1, ll2, Ontology = "MF", measure = "LP", dropCodes = NULL)
simUI(g1, g2)
simLP(g1, g2)

Arguments

ll1 A LocusLink ID as a character vector.
ll2 A LocusLink ID as a character vector.
Ontology Which ontology to use ("MF", "BP", "CC").
measure Which measure to use ("LP", "UI").
dropCodes A set of evidence codes to be ignored in constructing the induced GO graphs.
g1 An instance of the graph class.
g2 An instance of the graph class.

Details

For each of ll1 and ll2 the set of most specific GO terms within the ontology specified (Ontology) that are not based on any excluded evidence code (dropCodes) are found. Then the induced GO graphs are computed.

Finally these graphs are passed to one of simUI, (union intersection), or simLP (longest path). For simUI the distance is the size of the intersection of the node sets divided by the size of the union of the node sets. Large values indicate more similarity. These similarities are between 0 and 1.

For simLP the length of the longest path in the intersection graph of the two supplied graph. Again, large values indicate more similarity. Similarities are between 0 and the maximum leaf depth of the graph for the specified ontology.

Value

A list with:

sim The numeric similarity measure.
measure Which measure was used.
g1 The graph induced by ll1.
g2 The graph induced by ll2.


If one of the supplied Gene IDs does not have any GO terms associated with it, in the selected ontology and with the selected evidence codes then NA is returned.

Author(s)

R. Gentleman

See Also

makeGOGraph

Examples

  aa = simLL("9184", "3547", "BP")

[Package GOstats version 1.1.3 Index]