saddMBR: MBR of peptides

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

MBR of peptides

Description

MBR of peptides

Usage

saddMBR(
  base_name,
  ms1files,
  row_id = 1L,
  xsmat = NULL,
  ysmat = NULL,
  tsmat = NULL,
  ssmat = NULL,
  fsmat = NULL,
  nsmat = NULL,
  mbr_mzs,
  mbr_rets,
  mbr_peps,
  dat_dir,
  mbr_ret_tol = 25,
  gap = mbr_ret_tol + 90,
  min_y = 2e+06,
  yco = 100,
  step = 1e-05,
  fwhm_co = 0.5
)

Arguments

base_name	The base name of a peptide table file (TMTset[i]_LCMSinj[j]_Peptide_N.txt).
ms1files	A list of file names of retention-time calibrated RAW MS1 data corresponding to the peptide table at base_name (More than one file if with analyte pre-fractionation for a sample).
row_id	An integer corresponding to base_name, as well as the row number in xmat etc.
xsmat	A matrix of X (m-over-z) values under the peptide table at the base_name. The length is the number of peptides in the universe. NA values correspond to peptides (pep_seq_modz) that are not present in the current peptide table but found in others. Each cell in the matrix contains a list of all possible m-over-z candidates.
ysmat	A matrix of apex intensities.
tsmat	A matrix of apex retention times.
ssmat	A matrix of apex scan numbers.
fsmat	A matrix of FWHMs.
nsmat	A matrix of apex width in counts of MS2 scans.
mbr_mzs	A vector of m-over-z values in the universe (sample average).
mbr_rets	A vector of retention times in the universe (sample average).
dat_dir	The working data directory.
mbr_ret_tol	The tolerance in MBR retention time in seconds.
gap	A gap in retention-time window in seconds for finding gates in the Y values of LC. The gap value serves as a margin to trace out a whole peak with its apex within the mbr_ret_tol.
min_y	The cut-off of intensity values in MBR.
yco	The cut-off in Y-values.
step	The mass error in ppm / 1e6.
fwhm_co	The cut-off in FWHM values.

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