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Bimap objects and the Bimap interfaceDescriptionWhat we usually call "annotation maps" are in fact Bimap objects. In the following sections we present the bimap concept and the Bimap interface as it is defined in AnnotationDbi. Display methodsIn the code snippets below,
The bimap conceptA bimap is made of:
- 2 sets of objects: the left objects and the right objects.
All the objects have a name and this name is unique in
each set (i.e. in the left set and in the right set).
The names of the left (resp. right) objects are called the
left (resp. right) keys or the Lkeys (resp. the Rkeys).
- Any number of links (edges) between the left and right
objects. Note that the links can be tagged. In our model,
for a given bimap, either none or all the links are tagged.
In other words, a bimap is a bipartite graph. Here are some examples:
1. bimap B1:
4 left objects (Lkeys): "a", "b", "c", "d"
3 objects on the right (Rkeys): "A", "B", "C"
Links (edges):
"a" <--> "A"
"a" <--> "B"
"b" <--> "A"
"d" <--> "C"
Note that:
- There can be any number of links starting from or ending
at a given object.
- The links in this example are untagged.
2. bimap B2:
4 left objects (Lkeys): "a", "b", "c", "d"
3 objects on the right (Rkeys): "A", "B", "C"
Tagged links (edges):
"a" <-"x"-> "A"
"a" <-"y"-> "B"
"b" <-"x"-> "A"
"d" <-"x"-> "C"
"d" <-"y"-> "C"
Note that there are 2 links between objects "d" and "C":
1 with tag "x" and 1 with tag "y".
Flat representation of a bimapThe flat representation of a bimap is a data frame. For example, for B1, it is:
left right
a A
a B
b A
d C
If in addition the right objects have 1 multivalued attribute, for example, a numeric vector:
A <-- c(1.2, 0.9)
B <-- character(0)
C <-- -1:1
then the flat representation of B1 becomes:
left right Rattrib1
a A 1.2
a A 0.9
a B NA
b A 1.2
b A 0.9
d C -1
d C 0
d C 1
Note that now the number of rows is greater than the number of links! AnnDbBimap and FlatBimap objectsAn AnnDbBimap object is a bimap whose data are stored in a data base. A FlatBimap object is a bimap whose data (left keys, right keys and links) are stored in memory (in a data frame for the links). Conceptually, AnnDbBimap and FlatBimap objects are the same (only their internal representation differ) so it's natural to try to define a set of methods that make sense for both (so they can be manipulated in a similar way). This common interface is the Bimap interface. Note that both AnnDbBimap and FlatBimap objects have a read-only semantic: the user can subset them but cannot change their data. The "flatten" generic
flatten(x) converts AnnDbBimap object x into FlatBimap
object y with no loss of information
Note that a FlatBimap object can't be converted into an AnnDbBimap object (well, in theory maybe it could be, but for now the data bases we use to store the data of the AnnDbBimap objects are treated as read-only). This conversion from AnnDbBimap to FlatBimap is performed by the "flatten" generic function (with methods for AnnDbBimap objects only). Property0The "flatten" generic plays a very useful role when we need to understand or explain exactly what a given Bimap method f will do when applied to an AnnDbBimap object. It's generally easier to explain what it does on a FlatBimap object and then to just say "and it does the same thing on an AnnDbBimap object". This is exactly what Property0 says:
for any AnnDbBimap object x, f(x) is expected to be
indentical to f(flatten(x))
Of course, this implies that the f method for AnnDbBimap objects return the same type of object than the f method for FlatBimap objects. In this sense, the "revmap" and "subset" Bimap methods are particular because they are expected to return an object of the same class as their argument x, so f(x) can't be identical to f(flatten(x)). For these methods, Property0 says:
for any AnnDbBimap object x, flatten(f(x)) is expected to
be identical to f(flatten(x))
Note to the AnnotationDbi maintainers/developpers: the The Bimap interface in AnnotationDbiThe full documentation for the methods of the Bimap interface is splitted into 4 man pages: Bimap-direction, Bimap-keys and Bimap-toTable. See AlsoBimap-direction, Bimap-keys, Bimap-toTable, BimapFormatting, Bimap-envirAPI Exampleslibrary(hgu95av2.db) ls(2) hgu95av2GO # calls the "show" method summary(hgu95av2GO) hgu95av2GO2PROBE # calls the "show" method summary(hgu95av2GO2PROBE) Results
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> 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.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bimap
> ### Title: Bimap objects and the Bimap interface
> ### Aliases: Bimap Bimap class:Bimap Bimap-class AnnDbBimap
> ### class:AnnDbBimap AnnDbBimap-class GoAnnDbBimap class:GoAnnDbBimap
> ### GoAnnDbBimap-class Go3AnnDbBimap class:Go3AnnDbBimap
> ### Go3AnnDbBimap-class GOTermsAnnDbBimap class:GOTermsAnnDbBimap
> ### GOTermsAnnDbBimap-class AnnDbMap class:AnnDbMap AnnDbMap-class
> ### IpiAnnDbMap class:IpiAnnDbMap IpiAnnDbMap-class AgiAnnDbMap
> ### class:AgiAnnDbMap AgiAnnDbMap-class ProbeAnnDbBimap
> ### class:ProbeAnnDbBimap ProbeAnnDbBimap-class ProbeGo3AnnDbBimap
> ### class:ProbeGo3AnnDbBimap ProbeGo3AnnDbBimap-class ProbeAnnDbMap
> ### class:ProbeAnnDbMap ProbeAnnDbMap-class ProbeIpiAnnDbMap
> ### class:ProbeIpiAnnDbMap ProbeIpiAnnDbMap-class show,FlatBimap-method
> ### show,AnnDbBimap-method summary,Bimap-method summary,AnnDbBimap-method
> ### Keywords: classes interface
>
> ### ** Examples
>
> library(hgu95av2.db)
Loading required package: org.Hs.eg.db
> ls(2)
[1] "hgu95av2" "hgu95av2.db" "hgu95av2ACCNUM"
[4] "hgu95av2ALIAS2PROBE" "hgu95av2CHR" "hgu95av2CHRLENGTHS"
[7] "hgu95av2CHRLOC" "hgu95av2CHRLOCEND" "hgu95av2ENSEMBL"
[10] "hgu95av2ENSEMBL2PROBE" "hgu95av2ENTREZID" "hgu95av2ENZYME"
[13] "hgu95av2ENZYME2PROBE" "hgu95av2GENENAME" "hgu95av2GO"
[16] "hgu95av2GO2ALLPROBES" "hgu95av2GO2PROBE" "hgu95av2MAP"
[19] "hgu95av2MAPCOUNTS" "hgu95av2OMIM" "hgu95av2ORGANISM"
[22] "hgu95av2ORGPKG" "hgu95av2PATH" "hgu95av2PATH2PROBE"
[25] "hgu95av2PFAM" "hgu95av2PMID" "hgu95av2PMID2PROBE"
[28] "hgu95av2PROSITE" "hgu95av2REFSEQ" "hgu95av2SYMBOL"
[31] "hgu95av2UNIGENE" "hgu95av2UNIPROT" "hgu95av2_dbInfo"
[34] "hgu95av2_dbconn" "hgu95av2_dbfile" "hgu95av2_dbschema"
> hgu95av2GO # calls the "show" method
GO map for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
> summary(hgu95av2GO)
GO map for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
|
| Lkeyname: probe_id (Ltablename: probes)
| Lkeys: "1000_at", "1001_at", ... (total=12625/mapped=11242)
|
| Rkeyname: go_id (Rtablename: go_bpgo_ccgo_mf)
| Rkeys: "GO:0000002", "GO:0000003", ... (total=16339/mapped=14375)
|
| tagname: Evidence
|
| direction: L --> R
> hgu95av2GO2PROBE # calls the "show" method
GO2PROBE map for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
> summary(hgu95av2GO2PROBE)
GO2PROBE map for chip hgu95av2 (object of class "ProbeGo3AnnDbBimap")
|
| Lkeyname: probe_id (Ltablename: probes)
| Lkeys: "1000_at", "1001_at", ... (total=12625/mapped=11242)
|
| Rkeyname: go_id (Rtablename: go_bpgo_ccgo_mf)
| Rkeys: "GO:0000002", "GO:0000003", ... (total=16339/mapped=14375)
|
| tagname: Evidence
|
| direction: L <-- R
>
>
>
>
>
> dev.off()
null device
1
>
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