Methods for manipulating a Bimap object in a data-frame style

Description

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

Usage

  ## Extract all the columns of the map (links + right attributes)
  toTable(x)
  nrow(x)
  ncol(x)
  #dim(x)
  ## S4 method for signature 'FlatBimap'
head(x, ...)
  ## S4 method for signature 'FlatBimap'
tail(x, ...)

  ## Extract only the links of the map
  links(x)
  count.links(x)
  nhit(x)

  ## Col names and col metanames
  colnames(x, do.NULL=TRUE, prefix="col")
  colmetanames(x)
  Lkeyname(x)
  Rkeyname(x)
  keyname(x)
  tagname(x)
  Rattribnames(x)
  Rattribnames(x) <- value

Arguments

Details

toTable(x) turns Bimap object x into a data frame (see section "Flat representation of a bimap" in ?Bimap for a short introduction to this concept). For simple maps (i.e. no tags and no right attributes), the resulting data frame has only 2 columns, one for the left keys and one for the right keys, and each row in the data frame represents a link (or edge) between a left and a right key. For maps with tagged links (i.e. a tag is associated to each link), toTable(x) has one additional colmun for the tags and there is still one row per link. For maps with right attributes (i.e. a set of attributes is associated to each right key), toTable(x) has one additional colmun per attribute. So for example if x has tagged links and 2 right attributes, toTable(x) will have 5 columns: one for the left keys, one for the right keys, one for the tags, and one for each right attribute (always the rightmost columns). Note that if at least one of the right attributes is multivalued then more than 1 row can be needed to represent the same link so the number of rows in toTable(x) can be strictly greater than the number of links in the map.

nrow(x) is equivalent to (but more efficient than) nrow(toTable(x)).

ncol(x) is equivalent to (but more efficient than) ncol(toTable(x)).

colnames(x) is equivalent to (but more efficient than) colnames(toTable(x)). Columns are named accordingly to the names of the SQL columns where the data are coming from. An important consequence of this that they are not necessarily unique.

colmetanames(x) returns the metanames for the column of x that are not right attributes. Valid column metanames are "Lkeyname", "Rkeyname" and "tagname".

Lkeyname, Rkeyname, tagname and Rattribnames return the name of the column (or columns) containing the left keys, the right keys, the tags and the right attributes, respectively.

Like toTable(x), links(x) turns x into a data frame but the right attributes (if any) are dropped. Note that dropping the right attributes produces a data frame that has eventually less columns than toTable(x) and also eventually less rows because now exactly 1 row is needed to represent 1 link.

count.links(x) is equivalent to (but more efficient than) nrow(links(x)).

nhit(x) returns a named integer vector indicating the number of "hits" for each key in x i.e. the number of links that start from each key.

Value

A data frame for toTable and links.

A single integer for nrow, ncol and count.links.

A character vector for colnames, colmetanames and Rattribnames.

A character string for Lkeyname, Rkeyname and tagname.

A named integer vector for nhit.

Author(s)

H. Pages

See Also

Bimap, BimapFormatting, Bimap-envirAPI

Examples

  library(GO.db)
  x <- GOSYNONYM
  x
  toTable(x)[1:4, ]
  toTable(x["GO:0007322"])
  links(x)[1:4, ]
  links(x["GO:0007322"])

  nrow(x)
  ncol(x)
  dim(x)
  colnames(x)
  colmetanames(x)
  Lkeyname(x)
  Rkeyname(x)
  tagname(x)
  Rattribnames(x)

  links(x)[1:4, ]
  count.links(x)

  y <- GOBPCHILDREN
  nhy <- nhit(y) # 'nhy' is a named integer vector
  identical(names(nhy), keys(y)) # TRUE
  table(nhy)
  sum(nhy == 0) # number of GO IDs with no children
  names(nhy)[nhy == max(nhy)] # the GO ID(s) with the most direct children

  ## Some sanity check
  sum(nhy) == count.links(y) # TRUE

  ## Changing the right attributes of the GOSYNONYM map (advanced
  ## users only)
  class(x) # GOTermsAnnDbBimap
  as.list(x)[1:3]
  colnames(x)
  colmetanames(x)
  tagname(x) # untagged map
  Rattribnames(x)
  Rattribnames(x) <- Rattribnames(x)[3:1]
  colnames(x)
  class(x) # AnnDbBimap
  as.list(x)[1:3]

Results

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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-toTable.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Bimap-toTable
> ### Title: Methods for manipulating a Bimap object in a data-frame style
> ### Aliases: Bimap-toTable toTable toTable,FlatBimap-method
> ###   toTable,Bimap-method as.data.frame,Bimap-method nrow
> ###   nrow,Bimap-method nrow,FlatBimap-method nrow,AnnDbTable-method
> ###   nrow,AnnDbBimap-method nrow,Go3AnnDbBimap-method ncol
> ###   ncol,Bimap-method dim,Bimap-method head,FlatBimap-method
> ###   tail,FlatBimap-method links links,Bimap-method links,FlatBimap-method
> ###   links,AnnDbBimap-method links,Go3AnnDbBimap-method count.links
> ###   count.links,Bimap-method count.links,Go3AnnDbBimap-method nhit
> ###   nhit,Bimap-method nhit,environment-method nhit,list-method colnames
> ###   colnames,FlatBimap-method colnames,AnnDbBimap-method colmetanames
> ###   colmetanames,FlatBimap-method colmetanames,AnnDbBimap-method Lkeyname
> ###   Lkeyname,Bimap-method Lkeyname,AnnDbBimap-method Rkeyname
> ###   Rkeyname,Bimap-method Rkeyname,AnnDbBimap-method keyname
> ###   keyname,Bimap-method tagname tagname,Bimap-method
> ###   tagname,AnnDbBimap-method Rattribnames Rattribnames,Bimap-method
> ###   Rattribnames,AnnDbBimap-method Rattribnames<-
> ###   Rattribnames<-,FlatBimap-method Rattribnames<-,AnnDbBimap-method
> ###   Rattribnames<-,Go3AnnDbBimap-method
> ### Keywords: methods
> 
> ### ** Examples
> 
>   library(GO.db)

>   x <- GOSYNONYM
>   x
SYNONYM map for GO (object of class "GOTermsAnnDbBimap")
>   toTable(x)[1:4, ]
     synonym      go_id         Term Ontology
1 GO:0019952 GO:0000003 reproduction       BP
2 GO:0019952 GO:0000003 reproduction       BP
3 GO:0019952 GO:0000003 reproduction       BP
4 GO:0050876 GO:0000003 reproduction       BP
                                                                                                                    Definition
1 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
2 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
3 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
4 The production of new individuals that contain some portion of genetic material inherited from one or more parent organisms.
                             Synonym  Secondary
1 reproductive physiological process       <NA>
2                         GO:0019952 GO:0019952
3                         GO:0050876 GO:0050876
4 reproductive physiological process       <NA>
>   toTable(x["GO:0007322"])
     synonym      go_id                             Term Ontology
1 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
2 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
3 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
4 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
5 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
6 GO:0007322 GO:0000747 conjugation with cellular fusion       BP
                                                                                                                                                                          Definition
1 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
2 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
3 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
4 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
5 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
6 A conjugation process that results in the union of cellular and genetic information from compatible mating types. An example of this process is found in Saccharomyces cerevisiae.
      Synonym  Secondary
1 cell fusion       <NA>
2      mating       <NA>
3  GO:0007322 GO:0007322
4  GO:0007333 GO:0007333
5  GO:0030461 GO:0030461
6  GO:0030477 GO:0030477
>   links(x)[1:4, ]
     synonym      go_id
1 GO:0019952 GO:0000003
2 GO:0050876 GO:0000003
3 GO:0006594 GO:0000050
4 GO:0006871 GO:0000050
>   links(x["GO:0007322"])
     synonym      go_id
1 GO:0007322 GO:0000747
> 
>   nrow(x)
[1] 14176
>   ncol(x)
[1] 7
>   dim(x)
[1] 14176     7
>   colnames(x)
[1] "synonym"    "go_id"      "Term"       "Ontology"   "Definition"
[6] "Synonym"    "Secondary" 
>   colmetanames(x)
[1] "Lkeyname" "Rkeyname"
>   Lkeyname(x)
[1] "synonym"
>   Rkeyname(x)
[1] "go_id"
>   tagname(x)
[1] NA
>   Rattribnames(x)
[1] "Term"       "Ontology"   "Definition" "Synonym"    "Secondary" 
> 
>   links(x)[1:4, ]
     synonym      go_id
1 GO:0019952 GO:0000003
2 GO:0050876 GO:0000003
3 GO:0006594 GO:0000050
4 GO:0006871 GO:0000050
>   count.links(x)
[1] 1790
> 
>   y <- GOBPCHILDREN
>   nhy <- nhit(y) # 'nhy' is a named integer vector
>   identical(names(nhy), keys(y)) # TRUE
[1] TRUE
>   table(nhy)
nhy
    0     1     2     3     4     5     6     7     8     9    10    11    12 
11648  4318  4567  2775  1445   940   602   433   318   226   178   151   120 
   13    14    15    16    17    18    19    20    21    22    23    24    25 
   75    75    66    37    50    44    45    26    23    24    26    19    12 
   26    27    28    29    30    31    32    33    34    35    36    37    38 
    7    12    12    11    12     6     5     2     7    10     9     3     5 
   39    40    41    42    43    44    45    46    47    48    49    50    51 
    5    11     6     3     2     5     5     6     4     6     4     4     3 
   52    53    54    55    56    57    58    60    61    62    64    65    66 
    1     4     2     3     1     2     2     2     3     2     4     1     1 
   67    68    69    71    73    74    76    78    79    82    84    85    86 
    2     2     1     2     1     3     2     1     1     1     2     2     1 
   88    89    90    91    92    96    98   100   101   103   106   120   145 
    1     1     1     1     1     2     1     1     1     1     1     1     1 
  149   176   180   199   257   420 
    1     1     1     1     1     1 
>   sum(nhy == 0) # number of GO IDs with no children
[1] 11648
>   names(nhy)[nhy == max(nhy)] # the GO ID(s) with the most direct children
[1] "GO:0044767"
> 
>   ## Some sanity check
>   sum(nhy) == count.links(y) # TRUE
[1] TRUE
> 
>   ## Changing the right attributes of the GOSYNONYM map (advanced
>   ## users only)
>   class(x) # GOTermsAnnDbBimap
[1] "GOTermsAnnDbBimap"
attr(,"package")
[1] "AnnotationDbi"
>   as.list(x)[1:3]
$`GO:0000004`
GOID: GO:0008150
Term: biological_process
Ontology: BP
Definition: Any process specifically pertinent to the functioning of
    integrated living units: cells, tissues, organs, and organisms. A
    process is a collection of molecular events with a defined
    beginning and end.
Synonym: biological process
Synonym: physiological process
Synonym: GO:0000004
Synonym: GO:0007582
Secondary: GO:0000004
Secondary: GO:0007582

$`GO:0000021`
GOID: GO:0007131
Term: reciprocal meiotic recombination
Ontology: BP
Definition: The cell cycle process in which double strand breaks are
    formed and repaired through a double Holliday junction
    intermediate. This results in the equal exchange of genetic
    material between non-sister chromatids in a pair of homologous
    chromosomes. These reciprocal recombinant products ensure the
    proper segregation of homologous chromosomes during meiosis I and
    create genetic diversity.
Synonym: female meiotic recombination
Synonym: gene conversion with reciprocal crossover
Synonym: GO:0000021
Synonym: GO:0007145
Secondary: GO:0000021
Secondary: GO:0007145

$`GO:0000029`
GOID: GO:0006450
Term: regulation of translational fidelity
Ontology: BP
Definition: Any process that modulates the ability of the translational
    apparatus to interpret the genetic code.
Synonym: regulation of translational accuracy
Synonym: GO:0000029
Secondary: GO:0000029

>   colnames(x)
[1] "synonym"    "go_id"      "Term"       "Ontology"   "Definition"
[6] "Synonym"    "Secondary" 
>   colmetanames(x)
[1] "Lkeyname" "Rkeyname"
>   tagname(x) # untagged map
[1] NA
>   Rattribnames(x)
[1] "Term"       "Ontology"   "Definition" "Synonym"    "Secondary" 
>   Rattribnames(x) <- Rattribnames(x)[3:1]
>   colnames(x)
[1] "synonym"    "go_id"      "Definition" "Ontology"   "Term"      
>   class(x) # AnnDbBimap
[1] "AnnDbBimap"
attr(,"package")
[1] "AnnotationDbi"
>   as.list(x)[1:3]
$`GO:0000004`
[1] "GO:0008150"

$`GO:0000021`
[1] "GO:0007131"

$`GO:0000029`
[1] "GO:0006450"

> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>