idPoints {KCsmart}R Documentation

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}

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.

Value

Returns a data.frame listing the the position and the KC score for each identified point.

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)

Author(s)

Jorma de Ronde

See Also

plot

Examples

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))

[Package KCsmart version 1.6.0 Index]