kernelizeAll {macat} | R Documentation

## Smooth expression data for all chromosomes

### Description

'kernelizeAll' smoothes complete expression matrix and writes the result into one text file for each chromosome. These text files can be read into PYTHON.

### Usage

    kernelizeAll(data, step.width = 1e+05, kernel = rbf,
                 kernelparams = list(gamma = 1/10^13))

### Arguments

`data` | MACATData Object
`step.width` | size of steps for kernelization
`kernel` | kernel function one of rbf, kNN, basePairDistance or your owm
`kernelparams` | list of named kernel parameters

### Details

filename of the python flatfiles: `kernelized_seq_chrom_<chrom>.py` where <chrom> is the name of the chromosome.

### Value

produces text files

### Author(s)

The MACAT Development Team

### See Also

`pydata`, `kernelizeToPython`

### Examples

     ## Not run:
      # !!! take some time !!!
      loaddatapkg("stjudem")
      kernelizeAll(stjude)

    ## End(Not run)

[Package macat version 1.10.0 Index]