Last data update: 2014.03.03

 R: Methods for manipulating the keys of a Bimap object
Bimap-keysR Documentation

Methods for manipulating the keys of a Bimap object

Description

These methods are part of the Bimap interface (see ?Bimap for a quick overview of the Bimap objects and their interface).

Usage

  #length(x)
  isNA(x)
  mappedkeys(x)
  count.mappedkeys(x)
  keys(x) <- value
  #x[i]

Arguments

x

A Bimap object. If the method being caled is keys(x), then x can also be a AnnotationDb object or one of that objects progeny.

value

A character vector containing the new keys (must be a subset of the current keys).

i

A character vector containing the keys of the map elements to extract.

Details

keys(x) returns the set of all valid keys for map x. For example, keys(hgu95av2GO) is the set of all probe set IDs for chip hgu95av2 from Affymetrix.

Please Note that in addition to Bimap objest, keys(x) will also work for AnnotationDb objects and related objects such as OrgDb and ChipDb objects.

Note also that the double bracket operator [[ for Bimap objects is guaranteed to work only with a valid key and will raise an error if the key is invalid. (See ?`Bimap-envirAPI` for more information about this operator.)

length(x) is equivalent to (but more efficient than) length(keys(x)).

A valid key is not necessarily mapped ([[ will return an NA on an unmapped key).

isNA(x) returns a logical vector of the same length as x where the TRUE value is used to mark keys that are NOT mapped and the FALSE value to mark keys that ARE mapped.

mappedkeys(x) returns the subset of keys(x) where only mapped keys were kept.

count.mappedkeys(x) is equivalent to (but more efficient than) length(mappedkeys(x)).

Two (almost) equivalent forms of subsetting a Bimap object are provided: (1) by setting the keys explicitely and (2) by using the single bracket operator [ for Bimap objects. Let's say the user wants to restrict the mapping to the subset of valid keys stored in character vector mykeys. This can be done either with keys(x) <- mykeys (form (1)) or with y <- x[mykeys] (form (2)). Please note that form (1) alters object x in an irreversible way (the original keys are lost) so form (2) should be preferred.

All the methods described on this pages are "directed methods" i.e. what they return DOES depend on the direction of the Bimap object that they are applied to (see ?direction for more information about this).

Value

A character vector for keys and mappedkeys.

A single non-negative integer for length and count.mappedkeys.

A logical vector for isNA.

A Bimap object of the same subtype as x for x[i].

Author(s)

H. Pages

See Also

Bimap, Bimap-envirAPI, Bimap-toTable, BimapFormatting, AnnotationDb, select, columns

Examples

  library(hgu95av2.db)
  x <- hgu95av2GO
  x
  length(x)
  count.mappedkeys(x)
  x[1:3]
  links(x[1:3])

  ## Keep only the mapped keys
  keys(x) <- mappedkeys(x)
  length(x)
  count.mappedkeys(x)
  x # now it is a submap

  ## The above subsetting can also be achieved with
  x <- hgu95av2GO[mappedkeys(hgu95av2GO)]

  ## mappedkeys() and count.mappedkeys() also work with an environment
  ## or a list
  z <- list(k1=NA, k2=letters[1:4], k3="x")
  mappedkeys(z)
  count.mappedkeys(z)

  ## retrieve the set of primary keys for the ChipDb object named 'hgu95av2.db'
  keys <- keys(hgu95av2.db)
  head(keys)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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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(AnnotationDbi)
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/AnnotationDbi/Bimap-keys.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bimap-keys
> ### Title: Methods for manipulating the keys of a Bimap object
> ### Aliases: Bimap-keys keys,Bimap-method length,Bimap-method mappedkeys
> ###   mappedkeys,Bimap-method mappedkeys,environment-method
> ###   mappedkeys,vector-method count.mappedkeys
> ###   count.mappedkeys,Bimap-method count.mappedkeys,ANY-method isNA
> ###   isNA,Bimap-method isNA,environment-method isNA,ANY-method keys<-
> ###   keys<-,Bimap-method [,Bimap-method show,AnnDbTable-method
> ### Keywords: methods
> 
> ### ** Examples
> 
>   library(hgu95av2.db)
Loading required package: org.Hs.eg.db


>   x <- hgu95av2GO
>   x
GO map for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
>   length(x)
[1] 12625
>   count.mappedkeys(x)
[1] 11242
>   x[1:3]
GO submap for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
>   links(x[1:3])
     probe_id      go_id Evidence
1     1000_at GO:0000165      NAS
2     1000_at GO:0000165      TAS
3     1000_at GO:0000186      TAS
4     1000_at GO:0000187      TAS
5     1000_at GO:0000189      IEA
6     1000_at GO:0001934      IMP
7     1000_at GO:0002224      TAS
8     1000_at GO:0002755      TAS
9     1000_at GO:0002756      TAS
10    1000_at GO:0006360      TAS
11    1000_at GO:0006361      TAS
12    1000_at GO:0006461      IEA
13    1000_at GO:0006468      IDA
14    1000_at GO:0006915      IEA
15    1000_at GO:0006975      IDA
16    1000_at GO:0007049      IEA
17    1000_at GO:0007173      TAS
18    1000_at GO:0007264      TAS
19    1000_at GO:0007265      TAS
20    1000_at GO:0007411      TAS
21    1000_at GO:0007596      TAS
22    1000_at GO:0008286      TAS
23    1000_at GO:0008543      TAS
24    1000_at GO:0009636      IEA
25    1000_at GO:0010467      TAS
26    1000_at GO:0016032      IEA
27    1000_at GO:0016310      IDA
28    1000_at GO:0018105      IEA
29    1000_at GO:0019221      TAS
30    1000_at GO:0019233      IEA
31    1000_at GO:0019369      IEA
32    1000_at GO:0030168      TAS
33    1000_at GO:0030509      IMP
34    1000_at GO:0030878      IEA
35    1000_at GO:0031281      IMP
36    1000_at GO:0031663      IEA
37    1000_at GO:0032212      IMP
38    1000_at GO:0032872      TAS
39    1000_at GO:0033129      IMP
40    1000_at GO:0034134      TAS
41    1000_at GO:0034138      TAS
42    1000_at GO:0034142      TAS
43    1000_at GO:0034146      TAS
44    1000_at GO:0034162      TAS
45    1000_at GO:0034166      TAS
46    1000_at GO:0034605      TAS
47    1000_at GO:0035066      IMP
48    1000_at GO:0035666      TAS
49    1000_at GO:0038083      IDA
50    1000_at GO:0038095      TAS
51    1000_at GO:0038096      TAS
52    1000_at GO:0038123      TAS
53    1000_at GO:0038124      TAS
54    1000_at GO:0042473      IEA
55    1000_at GO:0043330      IEA
56    1000_at GO:0045087      TAS
57    1000_at GO:0045727      IEA
58    1000_at GO:0045944      IMP
59    1000_at GO:0048010      TAS
60    1000_at GO:0048011      TAS
61    1000_at GO:0048538      IEA
62    1000_at GO:0051090      TAS
63    1000_at GO:0051216      IEA
64    1000_at GO:0051403      TAS
65    1000_at GO:0051493      TAS
66    1000_at GO:0051973      IMP
67    1000_at GO:0060020      IEA
68    1000_at GO:0060324      IEA
69    1000_at GO:0060397      TAS
70    1000_at GO:0060425      IEA
71    1000_at GO:0060440      IEA
72    1000_at GO:0061308      IEA
73    1000_at GO:0070371      IEA
74    1000_at GO:0070374      IMP
75    1000_at GO:0070498      IMP
76    1000_at GO:0070849      IDA
77    1000_at GO:0071260      IEP
78    1000_at GO:0072584      TAS
79    1000_at GO:0090170      TAS
80    1000_at GO:1900034      TAS
81    1000_at GO:1904355      IMP
82    1000_at GO:2000641      TAS
83    1000_at GO:2000657      IEA
84    1001_at GO:0001525      IEA
85    1001_at GO:0001570      IEA
86    1001_at GO:0001701      IEA
87    1001_at GO:0007165      TAS
88    1001_at GO:0007498      TAS
89    1001_at GO:0016525      IEA
90    1001_at GO:0018108      IEA
91    1001_at GO:0018108      TAS
92    1001_at GO:0030336      IEA
93    1001_at GO:0032526      IEA
94    1001_at GO:0045026      IEA
95  1002_f_at GO:0006805      TAS
96  1002_f_at GO:0008202      IMP
97  1002_f_at GO:0016098      IDA
98  1002_f_at GO:0017144      IDA
99  1002_f_at GO:0019369      TAS
100 1002_f_at GO:0019373      IBA
101 1002_f_at GO:0019373      TAS
102 1002_f_at GO:0042738      IDA
103 1002_f_at GO:0044281      TAS
104 1002_f_at GO:0046483      IDA
105 1002_f_at GO:0055114      IDA
106 1002_f_at GO:0097267      TAS
107   1000_at GO:0005634      TAS
108   1000_at GO:0005635      IDA
109   1000_at GO:0005654      IDA
110   1000_at GO:0005654      TAS
111   1000_at GO:0005739      TAS
112   1000_at GO:0005769      TAS
113   1000_at GO:0005770      TAS
114   1000_at GO:0005794      TAS
115   1000_at GO:0005829      TAS
116   1000_at GO:0005856      TAS
117   1000_at GO:0005901      TAS
118   1000_at GO:0005925      TAS
119   1000_at GO:0015630      IDA
120   1000_at GO:0031143      IEA
121   1000_at GO:0043234      IEA
122   1000_at GO:0070062      IDA
123   1001_at GO:0005887      TAS
124 1002_f_at GO:0005789      TAS
125 1002_f_at GO:0043231      TAS
126   1000_at GO:0001784      IEA
127   1000_at GO:0004707      IDA
128   1000_at GO:0004707      NAS
129   1000_at GO:0004707      TAS
130   1000_at GO:0005515      IPI
131   1000_at GO:0005524      IEA
132   1000_at GO:0019902      IPI
133   1000_at GO:0097110      IEA
134   1001_at GO:0004714      IEA
135   1001_at GO:0005515      IPI
136   1001_at GO:0005524      IEA
137 1002_f_at GO:0004497      IDA
138 1002_f_at GO:0005506      IEA
139 1002_f_at GO:0008392      IBA
140 1002_f_at GO:0008395      IMP
141 1002_f_at GO:0016491      IDA
142 1002_f_at GO:0018675      IEA
143 1002_f_at GO:0018676      IEA
144 1002_f_at GO:0019825      TAS
145 1002_f_at GO:0019899      IPI
146 1002_f_at GO:0020037      IDA
147 1002_f_at GO:0052741      IEA
> 
>   ## Keep only the mapped keys
>   keys(x) <- mappedkeys(x)
>   length(x)
[1] 11242
>   count.mappedkeys(x)
[1] 11242
>   x # now it is a submap
GO submap for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
> 
>   ## The above subsetting can also be achieved with
>   x <- hgu95av2GO[mappedkeys(hgu95av2GO)]
> 
>   ## mappedkeys() and count.mappedkeys() also work with an environment
>   ## or a list
>   z <- list(k1=NA, k2=letters[1:4], k3="x")
>   mappedkeys(z)
[1] "k2" "k3"
>   count.mappedkeys(z)
[1] 2
> 
>   ## retrieve the set of primary keys for the ChipDb object named 'hgu95av2.db'
>   keys <- keys(hgu95av2.db)
>   head(keys)
[1] "1000_at"   "1001_at"   "1002_f_at" "1003_s_at" "1004_at"   "1005_at"  
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>


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