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]