Interpolation of pcf-estimates.
Given a segmentation by pcf, interpolate pcf-estimates for specific positions.
interpolate.pcf(segments,x)
segments |
a data frame containing the segmentation results from |
x |
matrix or data.frame where the first column gives chrosomomes and the second gives positions. |
Pcf-estimates are interpolated for the chromosomes and postions specified in x.
A data frame where the first two columns give the chromsomes and positions specified in the input x and the remaining columns give the interpolated pcf-estimate for each sample represented in segments.
The positions in segments and x must be of the same unit (bp, kbp, or mbp).
Gro Nilsen, Ole Christian Lingjaerde.
#Load the lymphoma data set: data(lymphoma) #Take out a smaller subset of 3 samples (using subsetData): sub.lymphoma <- subsetData(lymphoma,sample=1:3) #Run pcf: seg <- pcf(data=sub.lymphoma,gamma=12) #Make a matrix with two positions and chromosomes for which we want to #interpolate the pcf-estimate: pos <- c(2000000,50000000) chr <- c(1,2) x <- cbind(chr,pos) #Interpolate int.pcf <- interpolate.pcf(seg,x)
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