SYSargsList-class {systemPipeR} | R Documentation

## Class `"SYSargsList"`

### Description

S4 class container for storing parameters and information of command-line- or R-based workflow.

### Objects from the Class

Objects can be created by calls of the form `new("SYSargsList", ...)`.

### Slots

`sprconfig`:

  Object of class `"list"` storing all the config information for the project

`stepsWF`:

  Object of class `"list"` storing all the `SYSargs2` objects of the workflow

`statusWF`:

  Object of class `"list"` storing all the success and failure of each step in the workflow

`dependency`:

  Object of class `"list"` storing all the dependency steps in the workflow

`projectWF`:

  Object of class `"list"` storing all the `projectWF` information of the workflow

`targetsWF`:

  Object of class `"list"` storing all the targets files for each step in the workflow

`SEobj`:

  Object of class `"list"` storing all the SummarizedExperiment objects in the workflow

`outfiles`:

  Object of class `"list"` storing all the output files in the workflow

`targets_connection`:

  Object of class `"list"` storing all targets files connection in the workflow

### Methods

[

  `signature(x = "SYSargsList", i = "ANY", j = "ANY", drop = "ANY")`: subsetting of class with bracket operator

[[

  `signature(x = "SYSargsList", i = "ANY", j = "ANY")`: subsetting of class with bracket operator

[[<-

  `signature(x = "SYSargsList", i = "ANY", j = "ANY", value = "ANY")`: replacement method for `SYSargsList` class

$

  `signature(x = "SYSargsList")`: extracting slots elements by name

coerce

  `signature(from = "list", to = "SYSargsList")`: `as(list, "SYSargsList")`

coerce

  `signature(from = "SYSargsList", to = "list")`: `as(SYSargsList, "list")`

length

  `signature(x = "SYSargsList")`: extracts number of `SYSargs2` objects

names

  `signature(x = "SYSargsList")`: extracts slot names

show

  `signature(object = "SYSargsList")`: summary view of `SYSargsList` steps

sprconfig

  `signature(x = "SYSargsList")`: extract data from `sprconfig` slot

stepsWF

  `signature(x = "SYSargsList")`: extract data from `stepsWF` slot

statusWF

  `signature(x = "SYSargsList")`: extract data from `statusWF` slot

dependency

  `signature(x = "SYSargsList")`: extract data from `dependency` slot

projectWF

  `signature(x = "SYSargsList")`: extract data from `projectWF` slot

targetsWF

  `signature(x = "SYSargsList")`: extract data from `targetsWF` slot

sysargslist

  `signature(x = "SYSargsList")`: Coerce back to list `as(SYSargsList, "list")`

SEobj

  `signature(x = "SYSargsList")`: extract data from `SEobj` slot

cmdlist

  `signature(x = "SYSargsList")`: extracts data from `cmdlist` slot for each step

appendStep<-

  `signature(x = "SYSargsList")`: replacement method for append a step

appendStep<-

  `signature(x = "SYSargsList")`: replacement method for append a step

replaceStep<-

  `signature(x = "SYSargsList")`: replacement method for replace a step

renameStep<-

  `signature(x = "SYSargsList")`: replacement method for rename a step

yamlinput<-

  `signature(x = "SYSargs2")`: replacement method for `yamlinput` slot for each step

### Author(s)

Daniela Cassol and Thomas Girke

### See Also

`SYSargs2` and `initWF`

### Examples

    showClass("SYSargsList")
    ## Not run:
    ## Construct SYSargsList object from Rmd file
    library(systemPipeRdata)
    script <- system.file("extdata/workflows/rnaseq", "systemPipeRNAseq.Rmd", package="systemPipeRdata")
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    dir_path <- tempdir()
    SYSconfig <- initProject(projPath=dir_path, targets=targets, script=script, overwrite = TRUE)
    sysargslist <- initWF(sysconfig ="SYSconfig.yml")

    ## End(Not run)

[Package systemPipeR version 1.26.3 Index]