kernelizeToPython: Smooth expression values and write to file

In macat: MicroArray Chromosome Analysis Tool

Description

Smoothes expression data for one chromosome and writes the result into a text file, which can be read into PYTHON, or returns it without writing. 'kernelizeToPython' is the one-chromosome version of kernelizeAll.

Usage

kernelizeToPython(data, chrom, step.width = 1e+05, kernel = rbf, 
                  kernelparams = list(gamma = 1/10^13), saveToFile = TRUE)

Arguments

data	MACATData Object
chrom	kernelize all genes that are on this chromosome
step.width	widtrh of interploation steps
kernel	kernel function one of rbf, kNN, basePairDistance or your own
kernelparams	list of named kernel parameters
saveToFile	logical indicating wether to save as flat file or not

Details

filename of the flatfile: kernelized_seq_chrom_<chrom>.py where <chrom> is the name of the chromosome.

Value

returns kernelized expression matrix

Author(s)

The MACAT Development team

See Also

pydata, kernelizeAll

Examples

  ## Not run: 
   data(stjd)
   kernelized = kernelizeToPython(stjd, 3)
  
## End(Not run)  

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