pad_mq_channels: Pads MaxQuant TMT channels to the highest plex.

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

Pads MaxQuant TMT channels to the highest plex.

Description

Pads MaxQuant TMT channels to the highest plex.

Usage

pad_mq_channels(
  file = NULL,
  fasta = NULL,
  entrez = NULL,
  use_corrected_mqint = TRUE,
  pep_co = 0.01,
  ...
)

Arguments

file	A PSM file name.
fasta	Character string(s) to the name(s) of fasta file(s) with prepended directory path. The fasta database(s) need to match those used in MS/MS ion search. There is no default and users need to provide the correct file path(s) and name(s).
entrez	Character string(s) to the name(s) of entrez file(s) with prepended directory path. At the NULL default, a convenience lookup is available for species among c("human", "mouse", "rat"). For other species, users need to provide the file path(s) and name(s) for the lookup table(s). See also Uni2Entrez and Ref2Entrez for preparing custom entrez files.
use_corrected_mqint	A logical argument for uses with MaxQuant TMT. At the TRUE default, values under columns "Reporter intensity corrected..." in MaxQuant PSM results (msms.txt) will be used. Otherwise, "Reporter intensity" values without corrections will be used.
pep_co	The cut-off in MaxQuant PEP probabilities. Use a value \le 0 to bypass.
...	filter_dots.

qzhang503/proteoQ documentation built on Dec. 14, 2024, 12:27 p.m.