getUnifiedCN: Get copy number values of each new unified segment from a...

In macintyrelab/CNpare: Comparing tumour copy number profiles

Get copy number values of each new unified segment from a chromosome

Description

This function generates a vector with copy number values of each new segment, which has been defined using getNewSegments function. This function in used in unifySegments function, where unified copy number values in each new chromosome segments is obtained to generate a unified copy number table

Usage

getUnifiedCN(new_seg, data)

Arguments

new_seg	dataframe defining the new unified segments in a specific chromosome
data	dataframe with original segments of the sample in a specific chromosome

Value

dataframe with unified segment tables

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=250000)
new_cn<-getUnifiedCN(new_seg,posSeg[posSeg$chromosome==1,])

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