STRMPSWorkflow {STRMPS}

Workflow function

Description

The function takes an input file and performs all preliminary analyses. The function creates a series of objects which can be further analysed. An output folder can be provided to store the objects as .RData-files.

Usage

STRMPSWorkflow(input, output = NULL, continueCheckpoint = NULL,
  control = workflow.control())

Arguments

input

A path to a .fastq-file.

output

A directory where output-files are stored.

continueCheckpoint

Choose a checkpoint to continue from in the workflow. If NULL the function will run the entire workflow.

control

Function controlling non-crucial parameters and other control functions.

Value

If 'output' not provided the function simply returns the stringCoverageList-object. If an output is provided the function will store ALL created objects at the output-path, i.e. nothing is returned.

Examples

readPath <- system.file('extdata', 'sampleSequences.fastq', package = 'STRMPS')

STRMPSWorkflow(readPath,
               control = workflow.control(restrictType = "Autosomal",
                                          numberOfThreads = 1)
               )