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Count the number of quantitfied features.

Source: R/functions-MSnSet.R
nQuants.Rd

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.

Author

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))
#>         iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
#> BSA       2941.052   5174.721   8955.985  18023.287
#> ECA0172  17593.548  18545.620  19361.837  18328.237
#> ECA0435   9847.256  11115.636  11550.405  10158.590
#> ECA0452   1524.148   1399.897   1547.218   1563.230
#> ECA0469   2139.889   2071.378   2058.840   1999.391
#> ECA0621   1101.062   1124.167   1140.093   1191.805
head(exprs(msnset2) * (n/m))
#>         iTRAQ4.114 iTRAQ4.115 iTRAQ4.116 iTRAQ4.117
#> BSA       2941.052   5174.721   8955.985  18023.287
#> ECA0172  35187.095  37091.239  38723.673  36656.473
#> ECA0435   9847.256  11115.636  11550.405  10158.590
#> ECA0452   3048.295   2799.794   3094.437   3126.460
#> ECA0469   2139.889   2071.378   2058.840   1999.391
#> ECA0621   2202.124   2248.334   2280.186   2383.611