compute.sliding {macat} | R Documentation |
'compute.sliding' computes a smoothing of the expression data or scores along the chromosome using the specified kernel function. This function is also used within the 'evalScoring' function. 'plotSliding' creates a plot of the smoothed expression values / scores.
compute.sliding(data, chromosome, sample, kernel, kernelparams=NULL, step.width = 1e+06) plotSliding(data, chromosome, sample, kernel, kernelparams=NULL, step.width=1000000, ...)
data |
A MACATData list holding the Expression values and gene locations |
chromosome |
the chromosome to be smoothed |
sample |
the sample (patient) whose expression values are smoothed |
kernel |
a kernel function (one of rbf, kNN, basePairDistance or your own) |
kernelparams |
a list of named parameters for the kernel (by default estimated from the data) |
step.width |
the smoothing is computed stepwise every step.width basepairs (default is 100000) |
... |
further graphical parameters passed on to plot.default |
for compute.sliding
: a matrix of dimension (steps x 2) with
in the first column the locations in basepairs where an interpolation
is computed, and in the second column the smoothed values.
plotSliding
does not return anything and is merely called for
its side-effect producing the plot.
MACAT development team
data(stjd) # just compute smoothed values: smooth = compute.sliding(stjd, chromosome=3, sample=6, rbf, kernelparams=list(gamma=1/10^13)) # compute and plot smoothed values: plotSliding(stjd, chromosome=3, sample=6,rbf, kernelparams=list(gamma=1/10^13),pch=20, main="Chromosome 3")