kernelizeToPython {macat}R Documentation

Smooth expression values and write to file

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

  data(stjd)
  kernelized = kernelizeToPython(stjd, 3)

[Package macat version 1.10.0 Index]