workflow.control: Workflow default options

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

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.

svilsen/STRMPS documentation built on May 31, 2019, 7:55 a.m.