discreteKernelize {macat}R Documentation

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

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(stjd)
   discretizedKernelized = discreteKernelize(stjd, 13)

[Package macat version 1.16.0 Index]