rawFilter: Function to apply filtering based on raw counts / frequency

In jweile/tileseqMave: TileSeq MAVE Analysis pipeline

Function to apply filtering based on raw counts / frequency

Description

Function to apply filtering based on raw counts / frequency

Usage

rawFilter(
  msc,
  countThreshold,
  wtq = 0.95,
  cvm = 10,
  srOverride = FALSE,
  useWTfilter = FALSE,
  lpdCutoff = NA
)

Arguments

msc	dataframe containing the output of the 'mean.sd.count()' function.
countThreshold	the threshold of raw counts that must be met
wtq	wild-type quantile, the quantile of the WT above which the nonselect or select have to be to not be filtered (lest they be considered spurious), also the quantile of the median deviation-informed distribution around zero, at which we consider "excessive" WT levels.
cvm	coefficient of variation multiplier. Up to how much more than the expected CV do we accept as normal?

Value

a vector listing for each row in the table which (if any) filters apply, otherwise NA.

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