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

In Shicheng-Guo/CHAT: Clonal Heterogeneity Analysis Tool

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.

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.

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.

Author(s)

Bo Li

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)

Shicheng-Guo/CHAT documentation built on Oct. 30, 2019, 11:55 p.m.