1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
|
\name{getSYMBOL}
\alias{getSYMBOL}
\alias{getGO}
\alias{getGOdesc}
\alias{getPMID}
\alias{getLL}
\alias{getEG}
\alias{lookUp}
\alias{getUniqAnnItem}
\title{Functions to deal with Data Packages}
\description{
The functions documented here are intended to make it easier to map
from a set of manufacturers identifiers (such as you will get from the
chips etc) to other identifiers.
}
\usage{
getSYMBOL(x, data)
getLL(x, data)
getEG(x, data)
getGO(x, data)
getPMID(x, data)
getGOdesc(x, which)
lookUp(x, data, what, load = FALSE)
getUniqAnnItem()
}
\arguments{
\item{x}{The identifiers to be mapped (usually manufacturer)}
\item{data}{The basename of the meta-data package to be used.}
\item{what}{\code{what} a character string for the name of an
annotation element of an annotation data package}
\item{which}{\code{which} a character string in the form of MF, BP,
CC, or ANY to indicated the GO categories of interest}
\item{load}{A logical value indicating whether to attempt to load the
required annotation data package if it isn't already loaded.}
}
\details{
Users must supply the basename of the meta-data package that they
want to use to provide the mappings. The name of the meta-data
package is the same as the basename.
Appropriate translations are done. In some cases such as \code{getEG}
and \code{getSYMBOL} there will only be one match and a vector is
returned. In other cases such as \code{getPMID} and \code{getGO} there
may be multiple matches and a list is returned.
For \code{getGOdesc} \code{x} contains GO identifiers (not
manufacturer identifiers) and the output is a list of GOTerms objects,
if \code{which} specifies some subset of the ontologies (MF, BP or CC)
then only terms for that ontology are retained.
\code{lookUp} is a general function that can be used to look
up matches. All other translation functions use \code{lookUp}
A BioC annotation data package contains annotation data environments
whose names are package name (e. g. hgu95av2) + element name
(e. g. PMID). \code{what} must be one of the element names for the
given data package.
\code{getUniqAnnItem} keeps track of the annotation elements that have
one to one mappings.
}
\value{
Either a vector or a list depending on whether multiple values per
input are possible.
}
\author{R. Gentleman}
\seealso{\code{\link{mget}}}
\examples{
library("hgu95av2.db")
library("GO.db")
data(sample.ExpressionSet)
gN <- featureNames(sample.ExpressionSet)[100:105]
lookUp(gN, "hgu95av2", "SYMBOL")
# Same as lookUp for SYMBOL except the return is a vector
getSYMBOL(gN,"hgu95av2" )
gg <- getGO(gN, "hgu95av2")
lookUp(gg[[2]][[1]][["GOID"]], "GO", "TERM")
# Same as lookUp for TERM
getGOdesc(gg[[2]][[1]][["GOID"]], "ANY")
# For BP only
getGOdesc(gg[[2]][[1]][["GOID"]], "BP")
getEG(gN, "hgu95av2")
getPMID(gN, "hgu95av2")
}
\keyword{manip}
|
