updateBench {SummarizedBenchmark} | R Documentation

## Check/Update SummarizedBenchmark

### Description

Function to update or check status of `SummarizedBenchmark` results.

If only a `SummarizedBenchmark` object is specified, the function will check whether 'func', 'param', 'meta', 'post' or the 'pkg_vers' of the methods in the `BenchDesign` stored with the `SummarizedBenchmark` do not match values stored in the `colData`. By default, no methods will be executed to update results. To actually execute updates, set `dryrun = FALSE`.

If a `BenchDesign` object is specified in addition to a `SummarizedBenchmark` object, the function will check which methods in the new `BenchDesign` need to be executed to update the `SummarizedBenchmark` results. Again, by default, no methods will be executed unless `dryrun = FLASE` is specified.

Unless `reuseParams = FALSE` is specified, the parameters of the last execution session stored in the the `colData` of the `SummarizedBenchmark` object will be used.

### Usage

    updateBench(sb, bd = NULL, dryrun = TRUE, version = FALSE,
      keepAll = TRUE, reuseParams = TRUE, ...)

### Arguments

`sb` | a `SummarizedBenchmark` object
`bd` | a `BenchDesign` object
`dryrun` | logical whether to just print description of what would be updated rather than actually running any methods. (default = TRUE)
`version` | logical whether to re-run methods with only package version differences. (default = FALSE)
`keepAll` | logical whether to keep methods run in original `SummarizedBenchmark` but not in new `BenchDesign`. Only used if `bd` is not NULL. (default = TRUE)
`reuseParams` | logical whether to reuse parameters from `buildBench` call used to create `SummarizedBenchmark` object (if available). Directly specified `buildBench` parameters still take precedence. (default = TRUE)
`...` | optional parameters to pass to `buildBench`.

### Value

SumamrizedBenchmark object.

### Author(s)

Patrick Kimes

### See Also

`buildBench`

### Examples

    ## load example SummarizedBenchmark object
    data(allSB)
    sb <- allSB[[1]]

    ## check if results are out of date
    updateBench(sb)

    ## modify BenchDesign
    bd <- BenchDesign(sb)
    bd <- dropMethod(bd, "kallisto-default")

    ## check if results need to be updated with new BenchDesign
    updateBench(sb, bd)

[Package SummarizedBenchmark version 2.12.0 Index]