correctImpurities.proteinGroups: Performs purity correction on MaxQuant proteinGroups.txt data

In GoldfarbLab/TMTPurityCorrection: Corrects TMT reporter intensities for TMT impurities

Description

Performs purity correction on MaxQuant proteinGroups.txt data

Usage

correctImpurities.proteinGroups(
  summary,
  proteinGroups,
  impurities,
  msms,
  intensities,
  noise,
  use.razor = T,
  method = c("NNLS", "OLS"),
  noise.replacement.method = c("pre", "post", "none"),
  remain.missing = T,
  remove.missing.rows = T
)

Arguments

summary	data frame of summary.txt
proteinGroups	data frame of evidence.txt
impurities	data frame of impurities for a specific lot
msms	optional data frame of msms.txt to perform correction at spectrum level. Required for noiseband imputation.
intensities	data frame of TMT intensity values, raw file, and MS2 scan number
noise	optional data frame of TMT noiseband values, raw file, and MS2 scan number
use.razor	should razor peptides be used for protein quantification. Only used if msms is supplied.
method	purity correction method. Options = "NNLS" and "OLS"
noise.replacement.method	should the noiseband replace missing values before or after correction. Options = "pre", "post", and "none"
remain.missing	should missing values be set to 0 (missing) after correction or not. Only used if not doing noiseband imputation. True or False
remove.missing.rows	should rows containing all missing rows be removed or not. True or False

GoldfarbLab/TMTPurityCorrection documentation built on Jan. 7, 2022, 2:01 p.m.