haddApexRTs_allsets: Helper of adding apex retention times for all PSM tables

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

Helper of adding apex retention times for all PSM tables

Description

Inputs are at the levels of all TMTSet_LCMSInj.txt files.

Usage

haddApexRTs_allsets(
  filelist = NULL,
  ms1full_files = NULL,
  dat_dir = NULL,
  path_ms1 = NULL,
  rt_size = 240,
  rt_margin = 480,
  max_rt_delta = 240,
  max_n_apexes = 2L,
  data_type = "raw"
)

Arguments

filelist	The file names of PSM tables, e.g., TMTSet1_LCMSinj1_PSM_N.txt etc.
ms1full_files	The file names of ms1full_.rds.
dat_dir	The working directory.
path_ms1	The file path to ms1full_.rds.
rt_size	The width of each LC retention times in seconds. Made big, as an apex RT can be several minutes earlier to the reference RT (of an triggering MS2) in one run and several minutes later in another.
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.
max_n_apexes	The maximum number of apexes for consideration.
data_type	The type of MS data.

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