Description Usage Arguments Value Author(s) Examples
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.
1 | getSumDist(oo, p, sam.dat, method = "both", type = 1, para)
|
oo |
Origin Cluster, as returned from |
p |
AGP value. see |
sam.dat |
numeric matrix, as returned from |
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 |
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
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)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.