MSnbase: featureCV – R documentation

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featureCV

Calculates coeffivient of variation for features

Description

This function calculates the column-wise coefficient of variation (CV), i.e. the ration between the standard deviation and the mean, for the features in an MSnSet. The CVs are calculated for the groups of features defined by groupBy. For groups defined by single features, NA is returned.

Usage

featureCV(x, groupBy, na.rm = TRUE, norm = "none", suffix = NULL)

Arguments

`x`	An instance of class `MSnSet`.
`groupBy`	An object of class `factor` defining how to summarise the features.
`na.rm`	A `logical(1)` defining whether missing values should be removed.
`norm`	One of normalisation methods applied prior to CV calculation. See `normalise()` for more details. Here, the default is `'none'`, i.e. no normalisation.
`suffix`	A `character(1)` to be used to name the new CV columns. Default is `NULL` to ignore this. This argument should be set when CV values are already present in the `MSnSet` feature variables.

Value

A matrix of dimensions length(levels(groupBy)) by ncol(x) with the respecive CVs. The column names are formed by pasting CV. and the sample names of object x, possibly suffixed by .suffix.

Author(s)

Laurent Gatto and Sebastian Gibb

Examples

data(msnset)
msnset <- msnset[1:4]
gb <- factor(rep(1:2, each = 2))
featureCV(msnset, gb)
featureCV(msnset, gb, suffix = "2")

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release