normalize.features {SIAMCAT}R Documentation

Perform feature normalization

Description

This function performs feature normalization according to user- specified parameters.

Usage

normalize.features(siamcat,
    norm.method = c("rank.unit", "rank.std",
        "log.std", "log.unit", "log.clr"),
    norm.param = list(log.n0 = 1e-06, sd.min.q = 0.1,
        n.p = 2, norm.margin = 1),
    feature.type='filtered',
    verbose = 1)

Arguments

siamcat

an object of class siamcat-class

norm.method

string, normalization method, can be one of these: 'c('rank.unit', 'rank.std', 'log.std', 'log.unit', 'log.clr')

norm.param

list, specifying the parameters of the different normalization methods, see details for more information

feature.type

On which type of features should the function work? Can be either "original", "filtered", or "normalized". Please only change this paramter if you know what you are doing!

verbose

control output: 0 for no output at all, 1 for only information about progress and success, 2 for normal level of information and 3 for full debug information, defaults to 1

Details

There are five different normalization methods available:

The list entries in 'norm.param' specify the normalzation parameters, which are dependant on the normalization method of choice:

The function additionally allows to perform a frozen normalization on a different dataset. After normalizing the first dataset, the output list $par contains all parameters of the normalization. Supplying this list together with a new dataset will normalize the second dataset in a comparable way to the first dataset (e.g. by using the same mean for the features for z-score standardization)

Value

an object of class siamcat-class with normalized features

Examples

    # Example data
    data(siamcat_example)

    # Simple example
    siamcat_norm <- normalize.features(siamcat_example,
    norm.method='rank.unit')

    # log.unit example
    siamcat_norm <- normalize.features(siamcat_example,
    norm.method='log.unit', norm.param=list(log.n0=1e-05, n.p=1,
    norm.margin=1))

    # log.std example
    siamcat_norm <- normalize.features(siamcat_example,
    norm.method='log.std', norm.param=list(log.n0=1e-05, sd.min.q=.1))


[Package SIAMCAT version 1.2.1 Index]