MSnbase (version 1.20.7)

nQuants: Count the number of quantitfied features.

Description

This function counts the number of quantified features, i.e non NA quantitation values, for each group of features for all the samples in an "MSnSet" object. The group of features are defined by a feature variable names, i.e the name of a column of fData(object).

Usage

nQuants(x, groupBy)

Arguments

x

An instance of class "MSnSet".

groupBy

An object of class factor defining how to summerise the features. (Note that this parameter was previously named fcol and referred to a feature variable label. This has been updated in version 1.19.12 for consistency with other functions.)

Value

A matrix of dimensions length(levels(groupBy)) by ncol(x)A matrix of dimensions length(levels(factor(fData(object)[, fcol]))) by ncol(object) of integers.

Details

This function is typically used after topN and before combineFeatures, when the summerising function is sum, or any function that does not normalise to the number of features aggregated. In the former case, sums of features might be the result of 0 (if no feature was quantified) to n (if all topN's n features were quantified) features, and one might want to rescale the sums based on the number of non-NA features effectively summed.

Examples

data(msnset)
n <- 2
msnset <- topN(msnset, groupBy = fData(msnset)$ProteinAccession, n)
m <- nQuants(msnset, groupBy = fData(msnset)$ProteinAccession)
msnset2 <- combineFeatures(msnset,
                           groupBy = fData(msnset)$ProteinAccession,
                           fun = sum)
stopifnot(dim(n) == dim(msnset2))
head(exprs(msnset2))
head(exprs(msnset2) * (n/m))