BBUM_apply: Apply BBUM fitting and correction onto a data.frame

In wyppeter/bbum: BBUM correction for significance testing of p values

Apply BBUM fitting and correction onto a data.frame

Description

Wrapper/intermediate function between BBUM_corr and BBUM_DEcorr. For internal use of the package.

Usage

BBUM_apply(
  df,
  add_starts,
  only_start,
  limits,
  pBBUM.alpha,
  auto_outliers,
  rthres,
  rtrimmax,
  atrimmax,
  two_tailed,
  quiet
)

Arguments

df	data.frame input
add_starts	List of named vectors for additional starts of fitting algorithm beyond the default set.
only_start	Whether the algorithm should only use the given starts (add_starts) to fit.
limits	Named list of custom limits for specific paramters. Parameters not mentioned would be default values.
pBBUM.alpha	Cutoff level of BBUM-FDR-adjusted p values for significance testing. Only used here to generate appropriate default limits.
auto_outliers	Toggle automatic outlier trimming.
rthres	Threshold value of r parameter to trigger a failed r.pass value. For automatic trimming methods in other functions and not meant for use in isolation.
rtrimmax	Maximum fraction of data points allowed to be outliers in the background set of data (to be trimmed).
atrimmax	Maximum absolute number of data points allowed to be outliers in the background set of data (to be trimmed).
two_tailed	Toggle the "two-tailed" case of BBUM correction, if the background assumption is weak and bona fide hits in the background class are relevant. See Details. Default behavior is off.
quiet	Suppress printed messages and warnings.

wyppeter/bbum documentation built on Oct. 3, 2023, 3:29 p.m.