CHAT (version 1.1)

getDistToPath: Find nearest distance from a data point to a canonical line

Description

For a given point on BAF-LRR plot and a given canonical line, this function finds the nearest point on the line to the data point.

Usage

getDistToPath(x0, y0, x, y, type, nb, nt, strictness = 1.1, 
thr = 0.001, is.scaling = F, BAF.scale = 8)

Arguments

x0

x coordinate for the Origin Cluster

y0

y coordinate for the Origin Cluster

x

x coordinate for the data point

y

y coordinate for the data point

type

integer, ploidy indicator. 1, diploid; 2, tetraploid; 3, hexaploid

nb

number of minor alleles

nt

number of total alleles

strictness

noise tolerance for points with sAGP around 1. See getPara.sAGP() for details.

thr

numeric, see details.

is.scaling

logic. If TRUE, the function will rescale the BAF values so that it has the same dimension as LRR.

BAF.scale

numeric. If is.scaling is TRUE, this is the value to rescale BAF values.

Value

A list representing a canonical line and containing the following elements:

p.min

sAGP value of the nearest point (X) on L to the data point (A).

dist

distance from A to X.

x.min

x coordinate of X.

y.min

y coordinate of X.

Details

For a given data point A, and a canonical line L, this function first finds a point X on L that is closest to A, and designates the distance from A to X is the closest distance from A to L. This step is achieved by sequentially split the period of L and select the half that is closer to A. The argument thr is the sensitivity threshold to find X during this step.

Examples

x0=0.05
y0=0.2
x=0.15
y=0.45
## Find X on canonical line for hemizygous amplification:
getDistToPath(x0,y0,x,y,1,1,3)