identifySTRRegions.control: Control function for identifySTRRegions

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

Control function for identifySTRRegions

Description

A list containing default parameters passed to the identifySTRRegions function.

Usage

identifySTRRegions.control(
  colList = NULL,
  numberOfThreads = 4L,
  reversed = TRUE,
  includeReverseComplement = TRUE,
  combineLists = TRUE,
  removeEmptyMarkers = TRUE,
  matchPatternMethod = "mclapply",
  indels = FALSE,
  trace = FALSE
)

Arguments

colList	The position of the forward, reverse, and motifLength columns in the flanking region tibble/data.frame. If 'NULL' a function searches for the words 'forward', 'reverse', and 'motif' ot identify the columns.
numberOfThreads	The number of threads used by mclapply (stuck at '2' on windows).
reversed	TRUE/FALSE: In a revrse complementary run, should the strings/quality be reversed (recommended)?
includeReverseComplement	TRUE/FALSE: Should the function also search for the reverse complement DNA strand (recommended)?
combineLists	TRUE/FALSE: If 'includeReverseComplement' is TRUE, should the sets be combined?
removeEmptyMarkers	TRUE/FALSE: Should markers returning no identified regions be removed?
matchPatternMethod	Which method should be used to identify the flanking regions (only 'mclapply' implemented at the moment)?
indels	TRUE/FALSE: Allow indels as well as base mismatches?
trace	TRUE/FALSE: Show trace? Note: only used if bam list is supplied.

Value

A control list setting default behaviour.

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