SPUTNIK (version 1.1)

varTransform,msi.dataset-method: Variance stabilizing transformation.

Description

varTransform transforms the MS intensities in order to reduce heteroscedasticity.

Usage

# S4 method for msi.dataset
varTransform(object, method = "log")

Arguments

object

msi.dataset-class object. See msiDataset.

method

string (default = log). Transformation method. Valid values are:

• "log": log-transformation defined as log(x + 1)

• "sqrt": square-root transformation.

Value

msi.dataset-class object with transformed peaks intensities.

Examples

# NOT RUN {
## Load package
library("SPUTNIK")

## Create the msi.dataset-class object
sz <- c(5, 4)
x <- matrix(rnorm(sz[1] * sz[2] * 20), sz[1]*sz[2], 20)
x[x < 0] <- 0 # MS data is positive
mz <- sort(sample(100, ncol(x)))
msiX <- msiDataset(x, mz, sz[1], sz[2])

## Normalize and log-transform
msiX <- normIntensity(msiX, "median")
msiX <- varTransform(msiX, "log")

## Create the msi.dataset-class object
sz <- c(5, 4)
x <- matrix(rnorm(sz[1] * sz[2]), sz[1]*sz[2], 20)
x[x < 0] <- 0 # MS data is positive
mz <- sort(sample(100, ncol(x)))
msiX <- msiDataset(x, mz, sz[1], sz[2])

## Normalize using PQN
msiX <- normIntensity(msiX, "PQN")
# }