pepLFQ: LFQ of peptides

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

LFQ of peptides

Description

Peptides are unique to species.

Usage

pepLFQ(
  basenames,
  are_refs,
  are_smpls,
  xsmat,
  ysmat,
  tsmat,
  ssmat,
  mmat,
  ymat,
  tmat,
  smat,
  cmat,
  mbr_peps,
  mbr_sps,
  sp_centers,
  new_na_species = ".other",
  rt_tol = 30,
  mbr_ret_tol = 30,
  lfq_mbr = TRUE,
  reference_spec_counts = FALSE,
  step = 0.005,
  err_log2r = 0.25
)

Arguments

basenames	The base names of a peptide table files (TMTset[i]_LCMSinj[j]_Peptide_N.txt).
are_refs	Logical; are references or not.
are_smpls	Logical; are samples or not.
xsmat	A matrix of m-over-z values.
ysmat	A matrix of apex intensities.
tsmat	A matrix of apex retention times.
ssmat	A matrix of apex scan numbers.
mmat	A logical matrix of MBR status.
ymat	A matrix of (first-pass) apex Y values. The binning of local patterns by retention time intervals can have boundary effects by separating close retention times into bin indexes ge +1 or le -1. If the log2FC is by ymat is closer to a species center than newly derived log2FC from local patterns, use the Y values from the first pass.
tmat	A matrix of (first-pass) apex retention times.
smat	A matrix of (first-pass) apex scan numbers.
cmat	A matrix of spectrum counts.
mbr_peps	A vector of pep_seq_modz sequences in the universe.
mbr_sps	A vector of peptide species in the universe.
sp_centers	The centers of log2FC for each species; names: species, values: log2FC.
new_na_species	A replace value for NA species.
rt_tol	Error tolerance in retention times.
mbr_ret_tol	The tolerance in MBR retention time in seconds.
lfq_mbr	Logical; perform LFQ-MBR or not.
reference_spec_counts	Logical; reference protein spectrum counts or not.
step	The step size in binning retention times.
err_log2r	Not yet used. Error tolerance in log2FC.

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