defdMethods enumerates methods defined for a class in a package -- NEEDS WORK

defdMethods enumerates methods defined for a class in a package -- NEEDS WORK

defdMethods(cl, pkg = paste0("package:", cl), verbose = TRUE)

Arguments

cl	character(1) name of class
pkg	character(1) name of package where class is defined, defaults to 'package:classname' which works for major classes like SummarizedExperiment; package: will be prepended if missing from supplied value of pkg
verbose	logical(1) if TRUE (default) will issue a message enumerating superclasses.

Value

a data.frame instance with columns 'method', 'cl', 'pkg', 'nmeth4cl', counting the number of method-signature combinations for this method, and 'sigs', a list of lists of named signature elements (each element is a list of character vectors of method parameter types, named with parameter names)

Note

Users should consider how methods inherited from superclasses defined in other packages are also relevant to reports of this type. See the example.

Examples

# start with simple tabulation of package-specific methods
suppressPackageStartupMessages({
require("SingleCellExperiment")
})
scem = defdMethods("SingleCellExperiment")
#> superclasses RangedSummarizedExperiment, SummarizedExperiment, RectangularData, Vector, Annotated, vector_OR_Vector may provide additional relevant methods/signatures
head(scem)
#>          method                   cl                          pkg nmeth4cl
#> 1             [ SingleCellExperiment package:SingleCellExperiment        1
#> 2           [<- SingleCellExperiment package:SingleCellExperiment        1
#> 3        altExp SingleCellExperiment package:SingleCellExperiment        3
#> 4      altExp<- SingleCellExperiment package:SingleCellExperiment        3
#> 5   altExpNames SingleCellExperiment package:SingleCellExperiment        1
#> 6 altExpNames<- SingleCellExperiment package:SingleCellExperiment        1
#>                                                                                                                    sigs
#> 1                                                                x="SingleCellExperiment", i="ANY", j="ANY", drop="ANY"
#> 2                                              x="SingleCellExperiment", i="ANY", j="ANY", value="SingleCellExperiment"
#> 3 x="SingleCellExperiment", e="character", x="SingleCellExperiment", e="missing", x="SingleCellExperiment", e="numeric"
#> 4 x="SingleCellExperiment", e="character", x="SingleCellExperiment", e="missing", x="SingleCellExperiment", e="numeric"
#> 5                                                                                              x="SingleCellExperiment"
#> 6                                                                           x="SingleCellExperiment", value="character"
scem$method
#>  [1] "["                     "[<-"                   "altExp"               
#>  [4] "altExp<-"              "altExpNames"           "altExpNames<-"        
#>  [7] "altExps"               "altExps<-"             "cbind"                
#> [10] "coerce"                "colData"               "colLabels"            
#> [13] "colLabels<-"           "colPair"               "colPair<-"            
#> [16] "colPairNames"          "colPairNames<-"        "colPairs"             
#> [19] "colPairs<-"            "counts"                "counts<-"             
#> [22] "cpm"                   "cpm<-"                 "int_colData"          
#> [25] "int_colData<-"         "int_elementMetadata"   "int_elementMetadata<-"
#> [28] "int_metadata"          "int_metadata<-"        "logcounts"            
#> [31] "logcounts<-"           "mainExpName"           "mainExpName<-"        
#> [34] "normcounts"            "normcounts<-"          "objectVersion"        
#> [37] "parallel_slot_names"   "rbind"                 "reducedDim"           
#> [40] "reducedDim<-"          "reducedDimNames"       "reducedDimNames<-"    
#> [43] "reducedDims"           "reducedDims<-"         "rowData"              
#> [46] "rowPair"               "rowPair<-"             "rowPairNames"         
#> [49] "rowPairNames<-"        "rowPairs"              "rowPairs<-"           
#> [52] "rowSubset"             "rowSubset<-"           "show"                 
#> [55] "sizeFactors"           "sizeFactors<-"         "tpm"                  
#> [58] "tpm<-"                 "updateObject"          "weights"              
#> [61] "weights<-"            
scem["isSpike", "sigs"]
#> [[1]]
#> NULL
#> 
# now let's collect some related classes, with the objective of
# enumerating relevant coercion methods and their signatures
require("SummarizedExperiment")
se = defdMethods("SummarizedExperiment", verbose=FALSE)
rse = defdMethods("RangedSummarizedExperiment", "package:SummarizedExperiment", verbose=FALSE)
cmb = try(rbind(scem,se,rse))
require("dplyr")
#> Loading required package: dplyr
#> 
#> Attaching package: ‘dplyr’
#> The following object is masked from ‘package:Biobase’:
#> 
#>     combine
#> The following objects are masked from ‘package:GenomicRanges’:
#> 
#>     intersect, setdiff, union
#> The following object is masked from ‘package:GenomeInfoDb’:
#> 
#>     intersect
#> The following objects are masked from ‘package:IRanges’:
#> 
#>     collapse, desc, intersect, setdiff, slice, union
#> The following object is masked from ‘package:matrixStats’:
#> 
#>     count
#> The following objects are masked from ‘package:S4Vectors’:
#> 
#>     first, intersect, rename, setdiff, setequal, union
#> The following objects are masked from ‘package:BiocGenerics’:
#> 
#>     combine, intersect, setdiff, union
#> The following objects are masked from ‘package:stats’:
#> 
#>     filter, lag
#> The following objects are masked from ‘package:base’:
#> 
#>     intersect, setdiff, setequal, union
require("magrittr")
#> Loading required package: magrittr
tmp = (cmb %>% filter(method=="coerce"))
sl = (tmp %>% select(sigs))[[1]]
names(sl) = tmp$cl
sl
#> $SingleCellExperiment
#> [1] "from=\"RangedSummarizedExperiment\", to=\"SingleCellExperiment\""
#> [2] "from=\"SummarizedExperiment\", to=\"SingleCellExperiment\""      
#> 
#> $SummarizedExperiment
#> [1] "from=\"ExpressionSet\", to=\"SummarizedExperiment\""             
#> [2] "from=\"RangedSummarizedExperiment\", to=\"SummarizedExperiment\""
#> [3] "from=\"SummarizedExperiment\", to=\"ExpressionSet\""             
#> [4] "from=\"SummarizedExperiment\", to=\"RangedSummarizedExperiment\""
#> [5] "from=\"SummarizedExperiment\", to=\"SingleCellExperiment\""      
#> 
#> $RangedSummarizedExperiment
#> [1] "from=\"ExpressionSet\", to=\"RangedSummarizedExperiment\""       
#> [2] "from=\"RangedSummarizedExperiment\", to=\"ExpressionSet\""       
#> [3] "from=\"RangedSummarizedExperiment\", to=\"SingleCellExperiment\""
#> [4] "from=\"RangedSummarizedExperiment\", to=\"SummarizedExperiment\""
#> [5] "from=\"SummarizedExperiment\", to=\"RangedSummarizedExperiment\""
#>