combineFeaturesfor a more general overview of feature aggregation and examples.
iPQF(object, groupBy, low.support.filter = FALSE, ratio.calc = "sum", method.combine = FALSE, feature.weight = c(7, 6, 4, 3, 2, 1, 5)^2)
MSnSetcontaining absolute ion intensities.
logicalspecifying if proteins being supported by only 1-2 peptide spectra should be filtered out. Default is
"none"(don't calculate any ratios),
"sum"(default), or a specific channel (one of
sampleNames(object)) defining how to calculate relative peptides intensities.
logicaldefining whether to further use median polish to combine features.
"numeric"giving weight to the different features. Default is the squared order of the features redundant -unique-distance metric, charge state, ion intensity, sequence length, identification score, modification state, and mass based on a robustness analysis.
matrixwith estimated protein ratios.
data(msnset2) head(exprs(msnset2)) prot <- combineFeatures(msnset2, groupBy = fData(msnset2)$accession, fun = "iPQF") head(exprs(prot))