libraryQC: run library quality control (QC)

In jweile/tileseqMave: TileSeq MAVE Analysis pipeline

run library quality control (QC)

Description

run library quality control (QC)

Usage

libraryQC(
  dataDir,
  inDir = NA,
  outDir = NA,
  paramFile = paste0(dataDir, "parameters.json"),
  mc.cores = 6,
  srOverride = FALSE,
  wmThreshold = 5e-05,
  allCondOverride = FALSE,
  depthFilterOverride = FALSE
)

Arguments

dataDir	working data directory
inDir	input directory, defaults to subdirectory with latest timestamp ending in _mut_count.
outDir	output directory, defaults to name of input directory with _QC tag attached.
paramFile	input parameter file. defaults to <dataDir>/parameters.json
mc.cores	the maximum number of processes to run in parallel for multi-core processing. Warning: This also multiplies the amount of RAM used!
srOverride	override flag to allow for single-replicates
wmThreshold	'well-measuredness' threshold. The marginal frequency threshold at which variants are considered well-measured. Defaults to 5e-5, which roughly corresponds to the outdated definition in the legacy pipeline.
allCondOverride	override flag to run on ALL conditions instead of just the nonselect

Value

NULL. Results are written to file.

jweile/tileseqMave documentation built on April 5, 2024, 4:51 p.m.