nomadAssembleProteins: Assemble Protein abundance measurements from Peptide...

In carlmurie/NOMAD: Normalization of Mass Spectrometry Data

Description

Assemble Protein abundance measurements from Peptide abundance measurements

Usage

nomadAssembleProteins(y, x, method = "TukeyBW", format = "BySample",
  combineDupPeptides = FALSE, standardizeAbundance = FALSE,
  mySep = "&_MYSEP_&")

Arguments

y	vector Dependant variable (vector of real numbers)
x	vector Independent or explanatory variables (matrix). In this context they will be Peptide, Protein, Run, and iTRAQ identifiers. Run and iTRAQ identifiers must be numeric
method	string Method of calculating center of peptide abundances per protein - choices: TukeyBW, Median, or Mean. Default is TukeyBW
format	string BySample - each column is an individual sample ByProtein - rows are proteins-columns are abundance,day and itraq
combineDupPeptides	string If TRUE then average (based on method) duplicated peptides for the same protein before calculating protein abundance
standardizeAbundance	logical If TRUE then transform each sample (experiment and iTRAQ) with a robust Z adjustment. The default is FALSE.
mySep	logical Character string that must not exist in any factor in "x".

Value

List with elements scores matrix of normalized protein scores. each row is a protein and each column is a single sample (run and iTRAQ)

Examples

data(BalfPeptides)

ret <- nomadNormalization(y=BalfPeptides$Abundance, x=BalfPeptides)
scores <- nomadAssembleProteins(ret$y, ret$x)

carlmurie/NOMAD documentation built on May 14, 2019, 11:12 a.m.