idPoints: Identify points in sample point matrix plot
In KCsmart: Multi sample aCGH analysis package using kernel convolution

Description Usage Arguments Details Value Author(s) See Also Examples

Identify points in sample point matrix plot

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

`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

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.

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)

Jorma de Ronde

plot

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))