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", ...)
.
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
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
signature(from = "list", to = "SYSargsList")
: as(list, "SYSargsList")
signature(from = "SYSargsList", to = "list")
: as(SYSargsList, "list")
signature(x = "SYSargsList")
: extracts number of SYSargs2
objects
signature(x = "SYSargsList")
: extracts slot names
signature(object = "SYSargsList")
: summary view of SYSargsList
steps
signature(x = "SYSargsList")
: extract data from sprconfig
slot
signature(x = "SYSargsList")
: extract data from stepsWF
slot
signature(x = "SYSargsList")
: extract data from statusWF
slot
signature(x = "SYSargsList")
: extract data from dependency
slot
signature(x = "SYSargsList")
: extract data from projectWF
slot
signature(x = "SYSargsList")
: extract data from targetsWF
slot
signature(x = "SYSargsList")
: Coerce back to list as(SYSargsList, "list")
signature(x = "SYSargsList")
: extract data from SEobj
slot
signature(x = "SYSargsList")
: extracts data from cmdlist
slot for each step
signature(x = "SYSargsList")
: replacement method for append a step
signature(x = "SYSargsList")
: replacement method for append a step
signature(x = "SYSargsList")
: replacement method for replace a step
signature(x = "SYSargsList")
: replacement method for rename a step
signature(x = "SYSargs2")
: replacement method for yamlinput
slot for each step
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)