| 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) |
... |
futher graphical parameters passed on to plot |
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.
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")