SafeQuant (version 2.2.1)

getIBAQEset: Calculate intensity-based absolute-protein-quantification (iBAQ) metric per protein

Description

Calculate intensity-based absolute-protein-quantification (iBAQ) metric per protein

Usage

getIBAQEset(eset, proteinDB = NA, peptideLength = c(5, 36),
  nbMiscleavages = 0, proteaseRegExp = .getProteaseRegExp("trypsin"))

Arguments

eset

protein level ExpressionSet

proteinDB

list protein sequneces

peptideLength

peptide length interval (to get number of peptides used for normalization)

nbMiscleavages

number of mis-cleavages allowed when digesting protein sequneces in silico (to get number of peptides used for normalization)

proteaseRegExp

protease Reg Exp cleavage rule

Value

• ExpressionSet

Details

No details

References

Global quantification of mammalian gene expression control, Schwanhausser (2011), http://www.ncbi.nlm.nih.gov/pubmed/21593866, Critical assessment of proteome-wide label-free absolute abundance estimation strategies. Ahrne (2013), http://www.ncbi.nlm.nih.gov/pubmed/23794183

Examples

print("No examples")