discreteKernelize {macat} | R Documentation |
returns discretized kernelized expression values and saves them to a
file if argument 'saveToFile' is TRUE.
For details on discretization see discretize
.
discreteKernelize(data, chrom, margin = 10, step.width = 1e+05, kernel = rbf, kernelparams = list(gamma = 1/10^13), saveToFile = TRUE)
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 true |
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.
discretized and kernelized expression matrix
The MACAT Development team
#loaddatapkg("stjudem") data(stjd) discretizedKernelized = discreteKernelize(stjd, 13)