simLL: Functions to compute similarities between GO graphs and also...

In Bioconductor/GOstats: Tools for manipulating GO and microarrays

Functions to compute similarities between GO graphs and also between Entrez Gene 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,
      mapfun = NULL, chip = NULL)
simUI(g1, g2)
simLP(g1, g2)

Arguments

ll1	A Entrez Gene ID as a character vector.
ll2	A Entrez Gene 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.
mapfun	A function taking a character vector of Entrez Gene IDs as its only argument and returning a list of "GO lists" matching the structure of the lists in the GO maps of annotation data packages. The function should behave similarly to mget(x, eg2gomap, ifnotfound=NA), that is, NA should be returned if a specified Entrez ID has no GO mapping. See details for the interaction of mapfun and chip.
chip	The name of a DB-based annotation data package (the name will end in ".db"). This package will be used to generate an Entrez ID to GO ID mapping instead of mapfun.
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. The mapping is achieved in one of three ways:

1. If mapfun is provided, it will be used to perform the needed lookups. In this case, chip will be ignored.

2. If chip is provided and mapfun=NULL, then the needed lookups will be done based on the Entrez to GO mappings encapsulated in the specified annotation data package. This is the recommended usage.

3. If mapfun and chip are NULL or missing, then the function will attempt to load the GO package (the environment-based package, distinct from GO.db). This package contains a legacy environment mapping Entrez IDs to GO IDs. If the GO package is not available, an error will be raised. Omitting both mapfun and chip is not recommended as it is not compatible with the DB-based annotation data packages.

Next, 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

  library("hgu95av2.db")
  eg1 = c("9184", "3547")

  bb = simLL(eg1[1], eg1[2], "BP", chip="hgu95av2.db")

Bioconductor/GOstats documentation built on Nov. 2, 2024, 6:34 a.m.