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 1.12.0 Index]