rm_RToutliers: Cross-file removals of retention outliers

In qzhang503/proteoQ: Processing and Informatic Analysis of Mass Spectrometrirc Data

Cross-file removals of retention outliers

Description

Nullify X, Y, T(ime) and S(can) values if found as RT outliers (> 95 quantile of SD).

Usage

rm_RToutliers(
  pep_seq_modzs = NULL,
  pep_exp_mzs = NULL,
  pep_exp_ints = NULL,
  pep_apex_rets = NULL,
  pep_apex_scans = NULL,
  pep_apex_fwhm = NULL,
  pep_apex_n = NULL,
  mx = NULL,
  my = NULL,
  mt = NULL,
  ms = NULL,
  mf = NULL,
  mn = NULL,
  qt_rt = 0.95,
  ok_unv = FALSE,
  ignore_n2_outliers = FALSE,
  rt_tol = 0,
  by_fwhm = FALSE,
  fwhm_co = 0.5,
  qt_fwhm = 0.02,
  method = 0L
)

Arguments

pep_seq_modzs	List of peptide sequences with modifications and charge states.
pep_exp_mzs	List of m-over-z values. Each list element corresponds to entries in a df.
pep_exp_ints	List of intensity values.
pep_apex_rets	List of retention time values.
pep_apex_scans	List of apex scan numbers.
pep_apex_fwhm	List of apex FWHM values.
pep_apex_n	List of apex lengths (number of MS2 scans).
mx	The matrix of X values.
my	The matrix of Y values.
mt	The matrix of T values.
ms	The matrix of Scan values.
mf	The matrix of FWHM values.
mn	The matrix of N (numbers of scans) values.
qt_rt	The quantile for considering retention-time outliers.
ok_unv	Logical; is the universe ready or need to be compiled.
ignore_n2_outliers	Not yet used. Logical; ignore discrepant retention times at a two-sample scenario, for example, to retain a high-quality subset for RT calibrations.
rt_tol	Not yet used. The tolerance in retention times between two samples.
by_fwhm	Additional outlier removals by FWHM values.
fwhm_co	The cut-off in FWHM values.
qt_fwhm	The quantile for considering FWHM outliers.
method	A method for outlier removals.

qzhang503/proteoQ documentation built on Feb. 27, 2025, 8:34 a.m.