?Bimap for a quick overview of the Bimap
objects and their interface).They are divided in 2 groups: (1) methods for getting or setting the direction of a Bimap object and (2) methods for getting, counting or setting the left or right keys (or mapped keys only) of a Bimap object. Note that all the methods in group (2) are undirected methods i.e. what they return does NOT depend on the direction of the map (more on this below).
## Getting or setting the direction of a Bimap object
direction(x)
direction(x) <- value
revmap(x, ...)
## Getting, counting or setting the left or right keys (or mapped
## keys only) of a Bimap object
Lkeys(x)
Rkeys(x)
Llength(x)
Rlength(x)
mappedLkeys(x)
mappedRkeys(x)
count.mappedLkeys(x)
count.mappedRkeys(x)
Lkeys(x) <- value
Rkeys(x) <- value
"subset"(x, Lkeys = NULL, Rkeys = NULL, drop.invalid.keys = FALSE)
"subset"(x, Lkeys = NULL, Rkeys = NULL, drop.invalid.keys = FALSE, objName = NULL)direction(x) <- value.
A character vector containing the new keys (must be a subset of the
current keys) in Lkeys(x) <- value and Rkeys(x) <- value.
revmap and subset.
Extra argument for revmap can be:
objNamex is an
AnnDbBimap object).
Extra arguments for subset can be:
Lkeys
Rkeys
drop.invalid.keysdrop.invalid.keys=FALSE (the default), an error will be raised
if the new Lkeys or Rkeys contain invalid keys i.e. keys that don't belong
to the current Lkeys or Rkeys.
If drop.invalid.keys=TRUE, invalid keys are silently dropped.
objNamex is an
AnnDbBimap object).
1L or -1L for direction.A Bimap object of the same subtype as x for revmap
and subset.A character vector for Lkeys, Rkeys, mappedLkeys
and mappedRkeys.A single non-negative integer for Llength, Rlength,
count.mappedLkeys and count.mappedRkeys.
x that maps from left to right is
considered to be a direct map. Otherwise it is considered to be an
indirect map (when it maps from right to left). direction returns 1 on a direct map and -1
otherwise.
The direction of x can be changed with direction(x) <- value
where value must be 1 or -1.
An easy way to reverse a map (i.e. to change its direction) is to
do direction(x) <- - direction(x), or, even better, to use
revmap(x) which is actually the recommended way for doing it.
The Lkeys and Rkeys methods return respectively
the left and right keys of a Bimap object.
Unlike the keys method (see ?keys for
more information), these methods are direction-independent i.e. what
they return does NOT depend on the direction of the map.
Such methods are also said to be "undirected methods"
and methods like the keys method are said
to be "directed methods".
All the methods described below are also "undirected methods".
Llength(x) and Rlength(x) are equivalent to
(but more efficient than) length(Lkeys(x)) and
length(Rkeys(x)), respectively.
The mappedLkeys (or mappedRkeys) method returns
the left keys (or right keys) that are mapped to at least one right
key (or one left key).
count.mappedLkeys(x) and count.mappedRkeys(x) are
equivalent to (but more efficient than) length(mappedLkeys(x))
and length(mappedRkeys(x)), respectively. These functions give
overall summaries, if you want to know how many Rkeys correspond to a
given Lkey you can use the nhit function.
Lkeys(x) <- value and Rkeys(x) <- value are the
undirected versions of keys(x) <- value (see ?keys
for more information) and subset(x, Lkeys=new_Lkeys, Rkeys=new_Rkeys)
is provided as a convenient way to reduce the sets of left
and right keys in one single function call.
nhit
library(hgu95av2.db)
ls(2)
x <- hgu95av2GO
x
summary(x)
direction(x)
length(x)
Llength(x)
Rlength(x)
keys(x)[1:4]
Lkeys(x)[1:4]
Rkeys(x)[1:4]
count.mappedkeys(x)
count.mappedLkeys(x)
count.mappedRkeys(x)
mappedkeys(x)[1:4]
mappedLkeys(x)[1:4]
mappedRkeys(x)[1:4]
y <- revmap(x)
y
summary(y)
direction(y)
length(y)
Llength(y)
Rlength(y)
keys(y)[1:4]
Lkeys(y)[1:4]
Rkeys(y)[1:4]
## etc...
## Get rid of all unmapped keys (left and right)
z <- subset(y, Lkeys=mappedLkeys(y), Rkeys=mappedRkeys(y))
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