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)