addMethod {SummarizedBenchmark} | R Documentation

## Add method to BenchDesign object

### Description

Takes a `BenchDesign` object and the definition of a new method for benchmarking and returns the original `BenchDesign` with the new method included.

At a minimum, a method label (`label =`), and the workhorse function for the method (`func =`) must be specified for the new method.

Parameters for the method must be specified as a `quos` named list of `parameter = value` pairs mapping entries in the benchmarking data to the function parameters. For users familiar with the ggplot2 package, this can be viewed similar to the `aes =` mapping of data to geometry parameters.

An optional secondary function, `post`, can be specified if the output of the workhorse function, `func`, needs to be further processed. As an example, `post` may be a simple "getter" function for accessing the column of interest from the large object returned by `func`.

### Usage

    addMethod(bd, label, func, params = rlang::quos(), post = NULL,
      meta = NULL)

### Arguments

`bd` | `BenchDesign` object.
`label` | Character name for the method.
`func` | Primary function to be benchmarked.
`params` | Named quosure list created using `quos` of `parameter = value` pairs to be passed to `func`.
`post` | Optional post-processing function that takes results of `func` as input. Ignored if `NULL`. If multiple assays (metrics) should be generated for each method, this can be accomplished by specifying a named list of post-processing functions, one for each assay. (default = `NULL`)
`meta` | Optional metadata information for method to be included in `colData` of `SummarizedBenchmark` object generated using `link{buildBench}`. See Details for more information. Ignored if `NULL`. (default = `NULL`)

### Details

The optional `meta` parameter accepts a named list of metadata tags to be included for the method in the resulting `SummarizedBenchmark` object. This can be useful for two primary cases. First, it can help keep analyses better organized by allowing the specification of additional information that should be stored with methods, e.g. a tag for "method type" or descriptive information on why the method was included in the comparison. Second, and more improtantly, the `meta` parameter can be used to overwrite the package and version information that is automatically extracted from the function specified to `func`. This is particularly useful when the function passed to `func` is a wrapper for a script in (or outside of) R, and the appropriate package and version information can't be directly pulled from `func`. In this case, the user can either manually specify the `"pkg_name"` and `"pkg_vers"` values to `meta` as a list, or specify a separate function that should be used to determine the package name and version. If a separate function should be used, it should be passed to `meta` as a list entry with the name `pkg_func` and first quoted using `quo`, e.g. `list(pkg_func = quo(p.adjust))`.

### Value

Modified `BenchDesign` object with new method added.

### Author(s)

Patrick Kimes

### See Also

`modifyMethod`, `expandMethod`, `dropMethod`

### Examples

    ## create example data set of p-values
    df <- data.frame(pval = runif(100))

    ## example calculating qvalue from pvalues

    ## using standard call
    qv <- qvalue::qvalue(p = df$pval)
    qv <- qv$qvalue

    ## adding same method to BenchDesign
    bench <- BenchDesign(data = df)
    bench <- addMethod(bench,
                       label = "qv",
                        func = qvalue::qvalue,
                        post = function(x) { x$qvalue },
                        params = rlang::quos(p = pval))

[Package SummarizedBenchmark version 2.12.0 Index]