interpolate.pcf: Interpolation of pcf-estimates.

In igordot/copynumber: Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).

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)

igordot/copynumber documentation built on Sept. 18, 2020, 8:48 a.m.