colByCopyNumber {CopyNumberPlots} | R Documentation

## colByCopyNumber

### Description

Assign a color to each data element according to the copy number status of the its genomic location

### Usage

    colByCopyNumber(data, cn.calls, cn.column="cn", cn.colors=NULL)

### Arguments

`data` | The data elements. Can be a GRanges or anything accepted by `toGRanges`
`cn.calls` | The CN calls to use to select the color for the data elements
`cn.column` | The name of the column with the copy number information. (defaults to "cn")
`cn.colors` | The specification of the colors. Internally, it used to call the function getCopyNumberColors. Detailed documentation on color specification can be found there. (defaults to NULL)

### Details

Given a set of data elements positioned on the genome (either a GRanges or any other format accepted by regioneR's `toGRanges`) and a set of copy number calls, assign a color to each element depending on the copy number status of the genomic region where it's located. The colors can be customized using the `cn.colors` parameter as documented in getCopyNumberColors.

### Value

Return a vector of colors with the same length as the number of elements in data

### See Also

toGRanges, getCopyNumberColors, plotBAF

### Examples

    pos <- sort(floor(runif(1000, 1, 10000)))
    baf.data <- toGRanges("chr1", pos, pos)
    baf.data$baf <- rnorm(1000, mean = 0.5, sd = 0.05)
    baf.data$baf[1:400] <- baf.data$baf[1:400] + c(0.2, -0.2)

    breakpoint <- start(baf.data)[400]
    cn.calls <- toGRanges(data.frame(chr=c("chr1", "chr1"), start=c(1, breakpoint+1), end=c(breakpoint, 10000), cn=c(3,2)))

    kp <- plotKaryotype(zoom=toGRanges("chr1", 1, 10000))
    plotBAF(kp, baf.data, points.col = colByCopyNumber(baf.data, cn.calls))

[Package CopyNumberPlots version 1.3.3 Index]