macat (version 1.46.0)

discreteKernelize: 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

Value

discretized and kernelized expression matrix

Details

Filename of the flatfile is: discrete_kernelized_seq_margin__chrom_.py where is the discretization parameter and the name of the chromosome.

See Also

pydata, kernelizeAll

Examples

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