addApexRTs: Helper of adding apex retention times for one RAW

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

Helper of adding apex retention times for one RAW

Description

Inputs are at the levels of one RAW file.

Usage

addApexRTs(
  df,
  file_ms1,
  path_ms1,
  from = 115,
  step = 1e-05,
  rt_size = 240,
  rt_margin = 480,
  max_rt_delta = 240,
  yco = 100,
  min_y = 2e+06,
  n_para = 6L
)

Arguments

df	A subset of PSM table under one RAW.
file_ms1	The file name of an ms1full_.rds.
path_ms1	The file path to ms1full_.rds.
from	The starting point for calculating the bin indexes of masses.
step	A step size in mass for binning.
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_para	The number of parallel processes.

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