correctImpurities.RTS: Performs purity correction on TMT RTS data. The number of...

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

Description

Performs purity correction on TMT RTS data. The number of intensity columns must equal the number of reporters in the impurity file Output is a data frame of the same dimensions

Usage

correctImpurities.RTS(
  msms,
  impurities,
  noise,
  method = c("NNLS", "OLS"),
  noise.replacement.method = c("pre", "post"),
  remain.missing = T,
  remove.missing.rows = T,
  use.razor = T
)

Arguments

msms	data frame of uncorrected TMT intensities, raw file, and MS2 scan number
impurities	data frame of impurities for a specific lot
noise	optional data frame of TMT noiseband values, raw file, and MS2 scan number
method	purity correction method. Options = "NNLS" and "OLS"
noise.replacement.method	should the noiseband replace missing values before or after correction. Options = "pre" and "post"
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.