stringCoverage.control: String coverage coontrol object

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

String coverage coontrol object

Description

String coverage coontrol object

Usage

stringCoverage.control(
  numberOfThreads = 4L,
  simpleReturn = TRUE,
  uniquelyAssigned = TRUE,
  additionalFlags = FALSE,
  numberOfMutations = 1,
  includeAverageBaseQuality = FALSE,
  meanFunction = mean,
  trace = FALSE
)

Arguments

numberOfThreads	The number of cores used for parallelisation.
simpleReturn	TRUE/FALSE: Should the returned object be simplified?
uniquelyAssigned	TRUE/FALSE: Should regions which are not uniquely assigned be removed?
additionalFlags	TRUE/FALSE: Create additional flags for assessing sequence reliability?
numberOfMutations	the maximum number of mutations (base-calling errors) allowed during flanking region identification.
includeAverageBaseQuality	Should the average base quality of the region be included?
meanFunction	The function used to average the base qualities.
trace	TRUE/FALSE: Show trace?

Details

Control function for the 'stringCoverage' function. Sets default values for the parameters.

Value

List of parameters used for the 'stringCoverage' function.

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