R: Class '"SYSargsList"'

SYSargsList-class {systemPipeR}

R Documentation

Class `"SYSargsList"`

Description

SYSargsList S4 class is a list-like container where each instance stores all the input/output paths and parameter components required for a particular data analysis step based on command-line- or R-based software.

SYSargsList instances are constructed by the SYSargsList function.

Usage

## Accessors

stepsWF(x)
statusWF(x)
targetsWF(x)
outfiles(x)
SE(x, ...)
dependency(x)
projectInfo(x)
runInfo(x)

## Methods

cmdlist(x, ...)
codeLine(x, ...)
SampleName(x, ...)
stepName(x)
baseCommand(x, ...)
targetsheader(x, ...)
yamlinput(x, ...)
viewEnvir(x, silent = FALSE)
copyEnvir(x, list = character(), new.env = globalenv(), silent = FALSE)
addResources(x, step, resources)

## Subset Methods

subset(x, ...)
getColumn(x, step, position = c("outfiles", "targetsWF"), column = 1, 
          names = SampleName(x, step))

## Replacement

appendStep(x, after = length(x), ...) <- value
yamlinput(x, paramName, ...) <- value
replaceStep(x, step, step_name = "default") <- value
renameStep(x, step, ...) <- value
dependency(x, step, ...) <- value
appendCodeLine(x, after = length(x), ...) <- value
replaceCodeLine(x, line, ...) <- value
updateColumn(x, step, position = c("outfiles", "targetsWF")) <- value

Arguments

`x`	An instance of class `SYSargsList`.
`step`	character or numeric. Workflow step name or position index.
`silent`	If set to `TRUE`, all messages returned by the function will be suppressed.
`list`	a character vector naming objects to be copyied from the enviroment.
`new.env`	An environment to copy to. Default is `globalenv()`.
`resources`	`List` for reserving for each cluster job sufficient computing resources including memory (Megabyte), number of nodes (Int), CPU cores, walltime (Minutes), etc. It is necessary two additional files: `conffile` and `template`. `conffile` is the path to configuration file (default location `./.batchtools.conf.R`). This file contains in its simplest form just one command, such as this line for the scheduler: `cluster.functions <- makeClusterFunctionsSlurm(template="batchtools.slurm.tmpl")`. For more detailed information visit this page: https://mllg.github.io/batchtools/index.html. `template` The template files for a specific queueing/scheduling systems can be downloaded from here: https://github.com/mllg/batchtools/tree/master/inst/templates. Slurm, PBS/Torque, and Sun Grid Engine (SGE) templates are provided within the package demo data.
`position`	character. Options are `"outfiles" or "targetsWF"` slots.
`column`	character or numeric. Which column will be subset from the `position` argument.
`names`	character vector. Names of the workflow step.
`after`	A subscript, after which the values are to be appended.
`paramName`	character. Input name from `yamlinput(x)`, which value should be replaced.
`step_name`	character with the new step name. Default value will automatically give a name: `step_<step index position>`.
`line`	numeric. Index position of the code line to be added or replaced.
`value`	object containing the values to be replaced to `SYSargsList`. Values may be of the same class as the orginal values. For `updateColumn<-` a `DataFrame` must have the same rows as the original `DataFrame`. However, if there is no column/rows in the original `DataFrame`, the new `DataFrame` will replace the empty one. If there is a non-empty `DataFrame`, any existing columns with the same name as this new `DataFrame` will be replaced. Any columns that do not exist in the original `DataFrame` will be added to the original `DataFrame`.
`...`	Further arguments to be passed to or from other methods.

Objects from the Class

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

Slots

stepsWF:: Object of class "list" storing all the steps objects of the workflow. Each step can either be SYSargs2 or LineWise.
statusWF:: Object of class "list" storing all the success and failure of each step in the workflow.
targetsWF:: Object of class "list" storing all the targets DataFrame for each step in the workflow. For the LineWise steps, a DataFrame with 0 rows and 0 columns will be displayed.
outfiles:: Object of class "list" storing all the output DataFrame for each step in the workflow. For the LineWise steps, a DataFrame with 0 rows and 0 columns will be displayed.
SE:: Object of class "list" storing all the SummarizedExperiment objects in the workflow.
dependency:: Object of class "list" storing all the dependency graphs in the workflow.
projectInfo:: Object of class "list" storing all the projectInfo information of the workflow.
runInfo:: Object of class "list" storing all the runInfo information of each step 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"): extracting slots elements by name
coerce: signature(from = "list", to = "SYSargsList"): as(list, "SYSargsList")
coerce: signature(from = "SYSargsList", to = "list"): as(SYSargsList, "list")
sysargslist: signature(x = "SYSargsList"): Coerce back to list as(SYSargsList, "list")
length: signature(x = "SYSargsList"): extracts number of SYSargsList steps
names: signature(x = "SYSargsList"): extracts slot names
show: signature(object = "SYSargsList"): summary view of SYSargsList steps
stepsWF: signature(x = "SYSargsList"): extract data from stepsWF slot
statusWF: signature(x = "SYSargsList"): extract data from statusWF slot
targetsWF: signature(x = "SYSargsList"): extract data from targetsWF slot
outfiles: signature(x = "SYSargsList"): extract data from outfiles slot
SE: signature(x = "SYSargsList"): extract data from SE slot
dependency: signature(x = "SYSargsList"): extract data from dependency slot
projectInfo: signature(x = "SYSargsList"): extract data from projectInfo slot
runInfo: signature(x = "SYSargsList"): extract data from runInfo slot
cmdlist: signature(x = "SYSargsList", ...): extracts data from cmdlist slot for each SYSargs2 step
codeLine: signature(x = "SYSargsList", step): extracts data from codeLine slot for LineWise step
SampleName: signature(x = "SYSargsList", step): extracts Sample ID from SYSargs2 instance step
stepName: signature(x = "SYSargsList"): extracts steps names from workflow instance
baseCommand: signature(x = "SYSargsList", step): extracts baseCommand from SYSargs2 instance step
targetsheader: signature(x = "SYSargsList", step): extracts targetsheader from SYSargs2 instance step
yamlinput: signature(x = "SYSargsList", step): extracts data from yamlinput slot for each SYSargs2 step
viewEnvir: signature(x = "SYSargsList", silent = FALSE): return a vector of character strings giving the names of the objects in the SYSargsList environment
copyEnvir: signature(x = "SYSargsList", list = character(), new.env = globalenv(), silent = FALSE): copy of the contents or select objects from SYSargsList environment and place them into new.env
addResources: signature(x = "SYSargsList", step, resources): Adds the computing resources for one or multiple steps in the workflow. If the particular step(s) is set to be executed "management section," when the resources is added, the step(s) will be executed on the "compute section."
[[<-: signature(x = "SYSargsList", i = "ANY", j = "ANY", value = "ANY"): replacement method for SYSargsList class
appendStep<-: signature(x = "SYSargsList", after = length(x)): insert the SYSargsList or LineWise object onto x at the position given by after
yamlinput<-: signature(x = "SYSargsList", step, paramName ): replace a value in the yamlinput slot for a specific step instance
replaceStep<-: signature(x = "SYSargsList", step, step_name = "default"): replace a specific step in the workflow instance
renameStep<-: signature(x = "SYSargsList"): rename a stepName in the workflow instance
dependency<-: signature(x = "SYSargsList", step): replace dependency graph for a specific step instance
appendCodeLine<-: signature(x = "SYSargsList", step, after = length(x)): insert the R code in a specific step at the position given by after
replaceCodeLine<-: signature(x = "SYSargsList", step, line): replace the R code in a specific step at the position given by line
updateColumn<-: signature(x = "SYSargsList", step, position = c("outfiles", "targetsWF")): update or add a new column in targetsWF or outfiles slots

Author(s)

Daniela Cassol and Thomas Girke

Examples

sal <- SPRproject(overwrite=TRUE)
targetspath <- system.file("extdata/cwl/example/targets_example.txt", 
                            package="systemPipeR")

## Constructor and `appendStep<-`
appendStep(sal) <- SYSargsList(step_name = "echo", 
                               targets=targetspath, dir=TRUE,
                               wf_file="example/workflow_example.cwl", 
                               input_file="example/example.yml", 
                               dir_path = system.file("extdata/cwl", 
                               package="systemPipeR"),
                               inputvars = c(Message = "_STRING_",
                               SampleName = "_SAMPLE_"))
                               
appendStep(sal) <- LineWise(code = {
                            hello <- lapply(getColumn(sal, step=1, 'outfiles'), function(x) yaml::read_yaml(x))
                            }, 
                            step_name = "R_read", 
                            dependency = "echo")
sal 

length(sal)
names(sal)

## Accessors

stepsWF(sal)
statusWF(sal)
targetsWF(sal)
outfiles(sal)
SE(sal)
dependency(sal)
projectInfo(sal)
runInfo(sal)

## Methods

cmdlist(sal, step=1, targets=1:2) ## SYSargs2 step
codeLine(sal, step=2) ## LineWise step
SampleName(sal, step="echo")
stepName(sal)
baseCommand(sal, 1) ## SYSargs2 step
targetsheader(sal, step=1) ## SYSargs2 step
yamlinput(sal, step=1) ## SYSargs2 step
viewEnvir(sal)
copyEnvir(sal, list = character(), new.env = globalenv())

resources <- list(conffile= system.file("extdata/.batchtools.conf.R", 
                            package="systemPipeR"),
                  template= system.file("extdata/batchtools.slurm.tmpl", 
                            package="systemPipeR"),
                  Njobs=3, ## Usually, the samples number
                  walltime=60, ## minutes
                  ntasks=1,
                  ncpus=4, 
                  memory=1024 ## Mb
)
addResources(sal, 1, resources= resources)

## Subset Methods

sal_sub <- subset(sal, subset_steps=1, input_targets=1:2, keep_steps = TRUE)
sal_sub
targetsIn <- getColumn(sal, step=1, position = c("outfiles"))
targetsIn

## Replacement
renameStep(sal, step=1) <- "new_echo"
dependency(sal, step=2) <- "new_echo"
updateColumn(sal, step=2, position = c("targetsWF")) <- data.frame(targetsIn)
targetsWF(sal)

replaceStep(sal, step=2) <- LineWise(code = {
                            hello <- "Printing a new message"
                            }, 
                            step_name = "R_hello", 
                            dependency = "new_echo")
codeLine(sal)
yamlinput(sal, step=1, paramName="results_path") <- list(results_path=list(
                                            class="Directory", path="./data"))
cmdlist(sal, step = 1, targets = 1)
appendCodeLine(sal, step=2, after = 0) <- "log <- log(10)"
codeLine(sal, 2)
replaceCodeLine(sal, step=2, line=1) <- LineWise(code = {
                            log <- log(50)
                            })
codeLine(sal, 2)

[Package systemPipeR version 2.0.8 Index]

Class "SYSargsList"