idPoints {KCsmart} | R Documentation |
Identify points in sample point matrix plot
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
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))