SafeQuant (version 2.3)

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")