Interpolation of pcf-estimates.

Given a segmentation by pcf, interpolate pcf-estimates for specific positions.

Usage

interpolate.pcf(segments, x)

Arguments

segments

a data frame containing the segmentation results from pcf().

x

matrix or data.frame where the first column gives chrosomomes and the second gives positions.

Value

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.

Details

Pcf-estimates are interpolated for the chromosomes and postions specified in x.

Note

The positions in segments and x must be of the same unit (bp, kbp, or mbp).

See also

pcf()

Author

Gro Nilsen, Ole Christian Lingjaerde.

Examples

#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)
#> pcf finished for chromosome arm 1p 
#> pcf finished for chromosome arm 1q 
#> pcf finished for chromosome arm 2p 
#> pcf finished for chromosome arm 2q 
#> pcf finished for chromosome arm 3p 
#> pcf finished for chromosome arm 3q 
#> pcf finished for chromosome arm 4p 
#> pcf finished for chromosome arm 4q 
#> pcf finished for chromosome arm 5p 
#> pcf finished for chromosome arm 5q 
#> pcf finished for chromosome arm 6p 
#> pcf finished for chromosome arm 6q 
#> pcf finished for chromosome arm 7p 
#> pcf finished for chromosome arm 7q 
#> pcf finished for chromosome arm 8p 
#> pcf finished for chromosome arm 8q 
#> pcf finished for chromosome arm 9p 
#> pcf finished for chromosome arm 9q 
#> pcf finished for chromosome arm 10p 
#> pcf finished for chromosome arm 10q 
#> pcf finished for chromosome arm 11p 
#> pcf finished for chromosome arm 11q 
#> pcf finished for chromosome arm 12p 
#> pcf finished for chromosome arm 12q 
#> pcf finished for chromosome arm 13q 
#> pcf finished for chromosome arm 14q 
#> pcf finished for chromosome arm 15q 
#> pcf finished for chromosome arm 16p 
#> pcf finished for chromosome arm 16q 
#> pcf finished for chromosome arm 17p 
#> pcf finished for chromosome arm 17q 
#> pcf finished for chromosome arm 18p 
#> pcf finished for chromosome arm 18q 
#> pcf finished for chromosome arm 19p 
#> pcf finished for chromosome arm 19q 
#> pcf finished for chromosome arm 20p 
#> pcf finished for chromosome arm 20q 
#> pcf finished for chromosome arm 21q 
#> pcf finished for chromosome arm 22q 
#> pcf finished for chromosome arm 23p 
#> pcf finished for chromosome arm 23q 

#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)