discreteKernelize: Discretize and smooth expression values

In macat: MicroArray Chromosome Analysis Tool

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

Details

Filename of the flatfile is: discrete_kernelized_seq_margin_<margin>_chrom_<chrom>.py where <margin> is the discretization parameter and <chrom> the name of the chromosome.

Value

discretized and kernelized expression matrix

Author(s)

The MACAT Development team

See Also

pydata, kernelizeAll

Examples

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

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