getNewSegments: Create new segments for unifying profiles in a specific...

In macintyrelab/CNpare: Comparing tumour copy number profiles

Create new segments for unifying profiles in a specific chromosome

Description

This function creates unified and collapse segments within a window distance. This function in used in unifySegments function, where a table with new segments per chromosome is generated for generating a unified copy number table.

Usage

getNewSegments(ref, exp, window)

Arguments

ref	dataframe with segments of the reference sample
exp	dataframe with segments of the experimental model
window	boundary margin for smoothing segments. Default is 100000

Value

dataframe with new segments in a specific chromosome

Examples

posSeg=cells_segcn[cells_segcn$sample=="OVKATE",]
data=cells_segcn[cells_segcn$sample=="OV-90",]
new_seg<-getNewSegments(ref=posSeg[posSeg$chromosome==1,],
    exp=data[data$chromosome==1,],window=100000)

macintyrelab/CNpare documentation built on April 15, 2022, 4:46 a.m.