calcEnrichment: calculate logPhi enrichment ratios

In jweile/tileseqMave: TileSeq MAVE Analysis pipeline

calculate logPhi enrichment ratios

Description

performs error modelling and regularization, filtering and calculates logPhi enrichment values

Usage

calcEnrichment(
  dataDir,
  inDir = NA,
  outDir = NA,
  paramFile = paste0(dataDir, "parameters.json"),
  mc.cores = 6,
  srOverride = FALSE,
  bnOverride = FALSE,
  bcOverride = FALSE,
  useWTfilter = FALSE,
  nbs = 10000,
  pessimistic = TRUE,
  useQuorum = FALSE,
  useLPDfilter = 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	number of CPU cores to use in parallel
srOverride	single replicate override
bnOverride	bottleneck filter override

Value

NULL. Results are written to file.

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