SYSargsList-class: Class '"SYSargsList"'

In systemPipeR: systemPipeR: NGS workflow and report generation environment

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

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

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 SYSargs2 class

$

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

codeSteps

signature(x = "SYSargsList"): ...

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 SYSargsList objects

names

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

projectWF

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

show

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

statusWF

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

dataWF

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

stepsWF

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

SYSargs2_steps

signature(x = "SYSargsList"): extract data from SYSargs2_steps slot

sysargslist

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

sysconfig

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

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)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.