STRMPSWorkflow: Workflow function

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

Description

The function takes an input file and performs the entire analysis workflow described in (ADD REF). The function creates a series of objects needed for further analyses. 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 May 31, 2019, 7:55 a.m.