interpolate.pcf {copynumber} | R Documentation

## Interpolation of pcf-estimates.

### Description

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.

### Details

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

### 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`.

### Note

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

### Author(s)

Gro Nilsen, Ole Christian Lingjaerde.

### See Also

`pcf`

### 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)

    #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)

[Package copynumber version 1.28.0 Index]