nQuants {MSnbase} | R Documentation

## 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.)

### 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.

### 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.

### Author(s)

Laurent Gatto <lg390@cam.ac.uk>, Sebastian Gibb <mail@sebastiangibb.de>

### 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,
                               method = sum)
    stopifnot(dim(n) == dim(msnset2))
    head(exprs(msnset2))
    head(exprs(msnset2) * (n/m))

[Package MSnbase version 2.15.7 Index]