workflow.control: Workflow default options

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

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,
  trimRegions = TRUE,
  restrictType = NULL,
  trace = TRUE,
  variantDatabase = NULL,
  reduceSize = FALSE,
  additionalFlags = TRUE
)

Arguments

numberOfMutations	The maximum number of mutations (base-calling errors) allowed during flanking region identification.
numberOfThreads	The number of threads used by the mclapply-function (stuck at '2' on windows).
createdThresholdSignal	Noise threshold.
thresholdHomozygote	Homozygote threshold for genotype identification.
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.
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 containing columns for 'Marker', 'Type', and 'Region'.
reduceSize	TRUE/FALSE: Should the size of the data-set be reduced using the quality and the variant database?
additionalFlags	TRUE/FALSE: Should the 'flankingRegions'-object be used to extract additional information from the flanking regions of each string?

Value

List of default of options.

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