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
.
simLL(ll1, ll2, Ontology = "MF", measure = "LP", dropCodes = NULL, mapfun = NULL, chip = NULL)
simUI(g1, g2)
simLP(g1, g2)
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
.mapfun
.graph
class.graph
class.ll1
.ll2
.NA
is returned.
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:
mapfun
is provided, it will be used to perform the
needed lookups. In this case, chip
will be ignored.
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.
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.
makeGOGraph
library("hgu95av2.db")
eg1 = c("9184", "3547")
bb = simLL(eg1[1], eg1[2], "BP", chip="hgu95av2.db")
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