haddApexRTs_oneset: Helper of adding apex retention times for one PSM table

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

Helper of adding apex retention times for one PSM table

Description

Inputs are at the levels of one TMTSet_LCMSInj.txt file.

Usage

haddApexRTs_oneset(
  file_psm = NULL,
  files_ms1 = NULL,
  dat_dir = NULL,
  path_ms1 = NULL,
  max_n_apexes = 2L,
  from = 115,
  step = 1e-05,
  rt_size = 240,
  rt_margin = 480,
  max_rt_delta = 240,
  yco = 100,
  min_y = 2e+06,
  n_cores = 1L
)

Arguments

file_psm	The file names of a PSM table, e.g., TMTSet1_LCMSinj1_PSM_N.txt.
files_ms1	The file name of an ms1full_.rds.
dat_dir	The working directory.
path_ms1	The file path to ms1full_.rds.
max_n_apexes	The maximum number of apexes for consideration.
from	A starting mass.
step	A step size.
rt_size	The width of each LC retention times in seconds.
rt_margin	The bracketing margin before and after an LC retention time window.
max_rt_delta	The maximum allowance in retention-time difference between the identifying MS2 event and apex.
yco	The cut-off in intensities.
min_y	The minimum peak area.
n_cores	The number of parallel processes calling the current utility.

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