SYSargsList-class {systemPipeR} | R Documentation |
"SYSargsList"
S4 class container for storing parameters and information of command-line- or R-based workflow.
Objects can be created by calls of the form new("SYSargsList", ...)
.
sysconfig
:Object of class "list"
storing all the config information for the project
codeSteps
:Object of class "list"
storing all the code steps
of the workflow
stepsWF
:Object of class "numeric"
storing all the index steps levels in the workflow
dataWF
:Object of class "data.frame"
storing all the data steps in the workflow
SYSargs2_steps
: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
projectWF
:Object of class "list"
storing all the directories from the project
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 SYSargs2 class
signature(x = "SYSargsList")
: extracting slots elements by name
signature(x = "SYSargsList")
: ...
signature(from = "list", to = "SYSargsList")
: as(list, "SYSargsList")
signature(from = "SYSargsList", to = "list")
: as(SYSargsList, "list")
signature(x = "SYSargsList")
: extracts number of SYSargsList
objects
signature(x = "SYSargsList")
: extracts slot names
signature(x = "SYSargsList")
: extract data from projectWF
slot
signature(object = "SYSargsList")
: summary view of SYSargsList
steps
signature(x = "SYSargsList")
: extract data from statusWF
slot
signature(x = "SYSargsList")
: extract data from dataWF
slot
signature(x = "SYSargsList")
: extract data from stepsWF
slot
signature(x = "SYSargsList")
: extract data from SYSargs2_steps
slot
signature(x = "SYSargsList")
: Coerce back to list as(SYSargsList, "list")
signature(x = "SYSargsList")
: extract data from sysconfig
slot
Daniela Cassol and Thomas Girke
SYSargs2
and initWF
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)