Transform ranking index distribution.

Description

The function performs a transformation of the ranking index so that its distribution is suitable as independent variable of the logistic regression model.

Usage

indexTransform(index, method = "normalize")

Arguments

Details

Works for vector, matrices and data.frames. In the case of matrices the function transforms each column separately from the other ones.

Two methods are currently implemented:

- normalize:

transforms the index into quantiles of a normal distribution.

- standardize:

performs an statistical standardization by subtracting the mean and dividing by the standard deviation.

Value

A transformed index. Its class will be that of the the input object.

Author(s)

David Montaner dmontaner@cipf.es

See Also

transferIndex, uvGsa, mdPat

Examples

myIndex <- runif (1000)
myTransformedIndex <- indexTransform (myIndex)
plot (myIndex, myTransformedIndex)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(mdgsa)


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mdgsa/indexTransform.Rd_%03d_medium.png", width=480, height=480)
> ### Name: indexTransform
> ### Title: Transform ranking index distribution.
> ### Aliases: indexTransform
> ### Keywords: index ranking transform
> 
> ### ** Examples
> 
> myIndex <- runif (1000)
> myTransformedIndex <- indexTransform (myIndex)
> plot (myIndex, myTransformedIndex)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>