simulateExperiment: Title
In jweile/tileseqMave: TileSeq MAVE Analysis pipeline

simulateExperiment

R Documentation

Title

Description

Title

Usage

simulateExperiment(
  workdir,
  paramFile = paste0(workdir, "parameters.json"),
  poolCV = 0.2,
  poolLambda = 1,
  fitBias = 0,
  fitSpread = 4,
  nPlasmids = 5e+05,
  nClones = 5e+05,
  assaySD = 0.01,
  assayTime = 3,
  seqDepth = 5e+06,
  varcallErr = 3e-06
)

Arguments

`workdir`	current working directory
`paramFile`	parameter file
`poolCV`	coefficient of variation in original mutant pool
`poolLambda`	number of mutations per clone
`fitBias`	fitness bias (towards neutral or deleterious)
`fitSpread`	fitness spread (how strongly it tends to extremes)
`nPlasmids`	size of initial plasmid pool
`nClones`	number of clones to be used in each replicate pool
`assaySD`	the amount of noise in the assay
`assayTime`	the growth time in the assay
`seqDepth`	the sequencing depth for tileseq
`varcallErr`	the per-base variant calling error