PipR-class: PipR
In MPIIComputationalEpigenetics/muPipeR: muPipeR

PipR-class

R Documentation

PipR

Description

A class for managing analysis pipelines

Usage

PipR(baseDir)

Arguments

baseDir

base directory for the pipeline

Details

When constructing PipR objects, a base directory will be created that contains subdirectories for the pipeline status, log files, analysis results and temporary files. Internally a graph representation of the pipeline is used for handling dependencies between jobs. See the package vignette for examples and more details.

Slots

baseDir: Base directory for the analysis pipeline
logDir: Directory containing log files orginating from executing the analysis pipeline
srcDir: Directory containing source files for executing the analysis pipeline
resultDir: Directory containing results orginating from executing the analysis pipeline. This directory will contain subdirectories for each analysis step
statusDir: Directory where status information on the execution of the pipeline will be stored. This includes the PipR object itself and a graphical overview
tempDir: Directory containing temporary files orginating from executing the analysis pipeline
idHash: A (most likely) unique hash string identifying the anlysis pipeline
steps: A list containing details on the steps registered for the analysis pipeline. This list contains list with elements corresponding to job details, i.e. job name, status, result directory and associated Job and JobResult objects.
graph: igraph graph representation storing all steps in the pipeline as nodes and step dependencies as edges.

Methods

getDir,PipR-method: Getter for the base and subdirectories
addStep,PipR-method: Add an analysis step to the pipeline and register it for being executed.
getSteps,PipR-method: Get the names of analysis steps in the pipeline.
run,PipR-method: Run the analysis pipeline executing all registered, incomplete steps.
getGraph,PipR-method: Get a graph representation storing all steps in the pipeline as nodes and step dependencies as edges.
getGraph,PipR-method: Plot the graph representation of the pipeline.
initializePipeDir,PipR-method: Create the pipeline directory and it's subdirectories.
changePipeDir,PipR-method: Change the pipeline directory.
cleanup,PipR-method: Remove temproary and uninformative files.
resetStep,PipR-method: Undo a pipeline step and its dependend steps resetting its results.