# getSumDist: Compute the summation of distances In CHAT: Clonal Heterogeneity Analysis Tool

## Description

Canonical positions are set on a BAF-LRR plot with given AGP value. This function finds the distance from each data point to its nearest canonical position and returns the summation.

## Usage

 `1` ```getSumDist(oo, p, sam.dat, method = "both", type = 1, para) ```

## Arguments

 `oo` Origin Cluster, as returned from `getOrigin()` `p` AGP value. see `getGrid()` for details. `sam.dat` numeric matrix, as returned from `getSeg()` or `getSegChr()` `method` string, chosen from 'both','logR' and 'BAF', the column(s) from sam.dat to weigh the distance from a data point to canonical positions. If 'logR' or 'BAF', number of LRR or BAF markers will be used as weight. If 'both', geometric average of both numbers will be used. `type` integer, ploidy indicator. 1, diploid; 2, tetraploid; 3, hexaploid `para` list, parameters returned from `getPara()`

## Value

A list inherited from the list returned from `getCanonicalLines()`, with extra elements being:

 `SD` sum of distances `clist` indices of data points close to at least one regression line. `plist` indices of data points close to at least one canonical position.

Bo Li

## Examples

 ``` 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15``` ```data(A0SD.BAF) data(A0SD.LRR) seg.dat=c() for(CHR in c(8,9,10)){ baf=A0SD.BAF[A0SD.BAF[,2]==CHR,] lrr=A0SD.LRR[A0SD.LRR[,2]==CHR,] x=getSegChr(baf,lrr) seg.dat=rbind(seg.dat,x) } dd.dat=seg.dat[,2:8] rownames(dd.dat)=seg.dat[,1] mode(dd.dat)='numeric' para=getPara() oo=getOrigin(dd.dat,para=para) cali=getSumDist(oo,0.5,dd.dat,para=para) ```

CHAT documentation built on May 29, 2017, 10:32 p.m.