idPoints: Identify points in sample point matrix plot

Description

Identify points in sample point matrix plot

Usage

idPoints(spm, mode='pos', dev=2, chromosomes=NULL)

Arguments

spm

The sample point matrix object of which points are to be identified

mode

Determines which points will be identified: mode='pos' will identify points in gained regions, mode='neg' will identify points in lost regions

dev

The device on which the sample point matrix was plotted

chromosomes

If not all chromosomes contained in the sample point matrix were plotted (using the 'chromosomes' argument in the 'plot' command), the same chromosomes must be entered here as an argument

Value

KCscore: KCscore of the identified point
chromosome: Chromosome on which the identified point is located
chromPosition: Position on the chromosome of the identified point
colin: Co-linear location of the identified point (given the selected chromosomes)

Details

Using the mouse pointer points in a sample point matrix plot can be identified by left-clicking on the to-be-identified points. Right-clicking exits the selection and returns the selected points.

Examples

Run this code

data(hsSampleData)
data(hsMirrorLocs)

#spm1mb <- calcSpm(hsSampleData, hsMirrorLocs)

#plot(spm1mb, type=1)
#idPoints(spm1mb)

#x11()
#plot(spm1mb, chromosomes=c(1,2,5))
#idPoints(spm1mb, mode='neg', dev=3, chromosomes=c(1,2,5))