macat (version 1.46.0)

kernelizeAll: 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

Value

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

Details

filename of the python flatfiles: kernelized_seq_chrom_.py where is the name of the chromosome.

See Also

pydata, kernelizeToPython

Examples

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