kernelizeAll: Smooth expression data for all chromosomes

In macat: MicroArray Chromosome Analysis Tool

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

does not return anything; called for its side-effect that is to produce Python-readable text files

Author(s)

The MACAT Development Team

See Also

pydata, kernelizeToPython

Examples

 ## Not run: 
  # !!! takes quite some time !!!
  loaddatapkg("stjudem")
  data(stjude)
  kernelizeAll(stjude)
 
## End(Not run)

macat documentation built on Nov. 8, 2020, 5:44 p.m.