varTransform,msi.dataset-method | R Documentation |
varTransform
transforms the MS intensities in order to reduce heteroscedasticity.
## S4 method for signature 'msi.dataset' varTransform(object, method = "log", offsetZero = 1)
object |
msi.dataset-class object. See msiDataset. |
method |
string (default =
|
offsetZero |
numeric (default = 1). This value is added to all the peak intensities to take into accounts of the zeros. It must be positive. |
msi.dataset-class object with transformed peaks intensities.
## Load package library("SPUTNIK") ## Create the msi.dataset-class object sz <- c(40, 40) x <- matrix(rnorm(sz[1] * sz[2] * 20) * 1000, 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(40, 40) x <- matrix(rnorm(sz[1] * sz[2] * 20) * 1000, 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")
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