STRMPSWorkflow: Workflow function

In svilsen/STRMPS: Analysis of Short Tandem Repeat (STR) Massively Parallel Sequencing (MPS) Data

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
    )
)

svilsen/STRMPS documentation built on Feb. 22, 2025, 4:51 p.m.