macat (version 1.46.0)

kernelizeToPython: 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

Value

returns kernelized expression matrix

Details

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

See Also

pydata, kernelizeAll

Examples

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