STRMPS (version 0.6.8)

STRMPSWorkflowBatch: Batch wrapper for the workflow function

Description

The function takes an input directory and performs the entire analysis workflow described in (ADD REF). The function creates a series of objects needed for further analyses and stores them at the output location.

Usage

STRMPSWorkflowBatch(
  input,
  output,
  ignorePattern = NULL,
  continueCheckpoint = NULL,
  control = workflow.control()
)

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.

Arguments

input

A directory where fastq input-files are stored.

output

A directory where output-files are stored.

ignorePattern

A pattern parsed to grepl used to filter input strings.

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.