workflow.control {STRMPS}

Workflow default options

Description

Control object for workflow function returning a list of default parameter options.

Usage

workflow.control(numberOfMutations = 1, numberOfThreads = 4,
  createdThresholdSignal = 0.05, thresholdHomozygote = 0.4,
  internalTrace = FALSE, simpleReturn = TRUE, identifyNoise = FALSE,
  identifyStutter = FALSE, flankingRegions = NULL, useSTRaitRazor = FALSE,
  trimRegions = TRUE, restrictType = NULL, trace = TRUE,
  variantDatabase = NULL, reduceSize = FALSE)

Arguments

numberOfMutations

The maximum number of mutations (base-calling errors) allowed during flanking region identification.

numberOfThreads

The number of threads used by either the mclapply-function (stuck at '2' on windows) or STRaitRazor.

createdThresholdSignal

Noise threshold.

thresholdHomozygote

Homozygote threshold for genotype identiication.

internalTrace

Show trace.

simpleReturn

TRUE/FALSE: Should the regions be aggregated without including flanking regions?

identifyNoise

TRUE/FALSE: Should noise be identified.

identifyStutter

TRUE/FALSE: Should stutters be identified.

flankingRegions

The flanking regions used to identify the STR regions. If 'NULL' a default set is loaded and used.

useSTRaitRazor

TRUE/FALSE: Should the STRaitRazor command line tool (only linux is implemented) be used for flanking region identification.

trimRegions

TRUE/FALSE: Should the identified regions be further trimmed.

restrictType

A character vector specifying the marker 'Types' to be identified.

trace

TRUE/FALSE: Should a trace be shown?

variantDatabase

A tibble of 'trusted' STR regions.

reduceSize

TRUE/FALSE: Should the size of the data-set be reduced using the quality and the variant database?

Value

List of default of options.