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("111", "112")
      bb = simLL("9184", "3547", "BP")

[Package GOstats version 2.0.4 Index]