cleanPSMYTS: Clean up PSM intensity (Y), retention time (T) and scan...

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

Clean up PSM intensity (Y), retention time (T) and scan values (S)

Description

Clean up PSM intensity (Y), retention time (T) and scan values (S)

Usage

cleanPSMYTS(
  dfs,
  ymat,
  tmat,
  smat,
  fmat,
  nmat,
  xsmat = NULL,
  ysmat = NULL,
  tsmat = NULL,
  ssmat = NULL,
  fsmat = NULL,
  nsmat = NULL,
  key = "pep_seq_modz",
  update = TRUE,
  update2 = FALSE,
  cols = c("pep_tot_int", "N_I000", "I000", "pep_apex_ret", "pep_apex_scan",
    "pep_apex_fwhm", "pep_apex_n")
)

Arguments

dfs	A list of PSM tables.
ymat	A matrix of apex intensities.
tmat	A matrix of apex retention times.
smat	A matrix of apex scan numbers.
fmat	A matrix of apex FWHM values.
nmat	A matrix of apex peak widths measured by the number of MS1 scans.
xsmat	A matrix of sets of moverz values.
ysmat	A matrix of sets of apexes intensities.
tsmat	A matrix of sets of retention times.
ssmat	A matrix of sets of scan numbers.
fsmat	A matrix of sets of FWHM values.
nsmat	A matrix of sets of peak widths measured by the number of MS1 scans.
key	The column key for matching.
update	Logical; update retention times or not. FALSE if dfs are already RT calibrated and the purpose is to nullify bad entries according to tmat.
update2	Logical; update apex_xs etc. or not. TRUE if the same pep_seq_modz corresponds to different sets of apex_ys, apex_ts etc. Also require update = TRUE to have an effect.
cols	The column keys for value updates.

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