discreteKernelize {macat} | R Documentation

## Discretize and smooth expression values

### Description

returns discretized kernelized expression values and saves them to a file if argument 'saveToFile' is TRUE. For details on discretization see `discretize`.

### Usage

    discreteKernelize(data, chrom, margin = 10, step.width = 1e+05, kernel = rbf,
                      kernelparams = list(gamma = 1/10^13), saveToFile = FALSE)

### Arguments

`data` | MACATData Object
`chrom` | chromosome to kernelize
`margin` | symmetric qunatile in percent
`step.width` | size of the interpolation steps
`kernel` | kernel function one of rbf, kNN, basePairDistance or your own
`kernelparams` | list of named kernel parameters
`saveToFile` | logicval indicating whether to write a flatfile or not; default is FALSE

### Details

Filename of the flatfile is: `discrete_kernelized_seq_margin_<margin>_chrom_<chrom>.py` where <margin> is the discretization parameter and <chrom> the name of the chromosome.

### Value

discretized and kernelized expression matrix

### Author(s)

The MACAT Development team

### See Also

`pydata`, `kernelizeAll`

### Examples

       #loaddatapkg("stjudem")
       data(stjd)
       discretizedKernelized = discreteKernelize(stjd, 13)

[Package macat version 1.14.0 Index]