IdMap is an object encapsulating a data frame
with two columns (Primary ID and Secondary ID)
where primaryID is a character string uniquely identifying the ID under consideration
(unprot accessions ID or acc, Entrez Gene ID etc) and the Secondary ID is a
comma separated list of secondary IDs associated with a given primary ID for a
particular DB service. The analysis typically starts from obtaining a set of ID Maps
(from the various DB services) which are not assumed to have the same number
of rows or the same set of primary IDs. The process of alignment of this ID Maps
is performed within the JointIdMap
A data.frame consisting of two columns (primary and secondary IDs) from which the IdMap object is to be created.
name
A character string representing the name of the given IdMap object. Default is ”
primaryKey
The name of the primary (first) column in an ID Map.
If missing then the input data frame first column name is used and if it is not available defaults to 'From'.
secondaryKey
The name of secondary (second) column in an ID Map.
If missing then the input data frame second column name is used and if it is not available defaults to 'To'.
...
Not used.
Fields and Methods
Methods:
as
-
as.UniquePairs
Create a UniquePairs object from a given IdMap object.
as.list
Coerce an object or a list of compatible object
.
getCounts
Compute the count of secondaryIDs for each primary ID.
merge
Merge the IdMap object with a second IdMap object or a list of IdMap objects.
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'license()' or 'licence()' for distribution details.
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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(IdMappingAnalysis)
Loading required package: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.20.0 (2016-02-17) successfully loaded. See ?R.oo for help.
Attaching package: 'R.oo'
The following objects are masked from 'package:methods':
getClasses, getMethods
The following objects are masked from 'package:base':
attach, detach, gc, load, save
Loading required package: rChoiceDialogs
Loading required package: rJava
Attaching package: 'rJava'
The following object is masked from 'package:R.oo':
clone
This is rChoiceDialogs 1.0.6 2014-09-05
This is IdMappingAnalysis 1.16.0 2013-05-24
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/IdMappingAnalysis/IdMap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: IdMap
> ### Title: The ID Map class
> ### Aliases: IdMap
> ### Keywords: classes
>
> ### ** Examples
>
> obj<-IdMap(examples$identDfList[[2]]);
> obj$primaryKey();
[1] "Uniprot"
> obj$secondaryKey();
[1] "Affy"
>
>
>
>
>
> dev.off()
null device
1
>