chromosomeCNplots {Repitools} | R Documentation

## Plot copy number by chromosome

### Description

Generates plots of position along chromosomes vs. estimated copy number. If GC adjustment was performed, then there are two plots per page; one before adjustment and one after adjustment.

### Usage

      ## S4 method for signature 'CopyEstimate'
    chromosomeCNplots(copy, y.max = NULL, pch = 19, cex = 0.2,
                 pch.col = "black", seg.col = "red", lty = 1, lwd = 2, verbose = TRUE)
      ## S4 method for signature 'AdjustedCopyEstimate'
    chromosomeCNplots(copy, y.max = NULL, pch = 19, cex = 0.2,
                 pch.col = "black", seg.col = "red", lty = 1, lwd = 2, verbose = TRUE)

### Arguments

`copy` | A `CopyEstimate` or `AdjustedCopyEstimate` object.
`y.max` | The maximum value of the y-axis of the scatter plots.
`pch` | Style of points in the scatter plots.
`cex` | Whether to square root the absolute copy number estimates before running the segmentation.
`pch.col` | Colour of points in the scatter plots.
`seg.col` | Colour of copy number segmentation line.
`lty` | Line type of plotted regression line.
`lwd` | Line width of plotted regression line.
`verbose` | Whether to print the progess of processing.

### Details

See `absoluteCN` or `relativeCN` for how to do the GC adjusted copy number estimates, if this is required. The segmentation line plotted is of the segmentation regions found by circular binary segmentation.

### Value

A number of pages of scatterplots. The output should, therefore, be sent to a PDF device.

### Author(s)

Dario Strbenac

### Examples

      ## Not run:
        library(BSgenome.Hsapiens.UCSC.hg18)
        library(BSgenome.Hsapiens36bp.UCSC.hg18mappability)
        load("inputsReads.RData")
        windows <- genomeBlocks(Hsapiens, chrs = paste("chr", c(1:22, 'X', 'Y'), sep = ''),
                                width = 20000)
        counts <- annotationBlocksCounts(inputsReads, anno = windows, seq.len = 300)

        gc.par <- GCAdjustParams(genome = Hsapiens, mappability = Hsapiens36bp,
                                 min.mappability = 50, n.bins = 10, min.bin.size = 10,
                                 poly.degree = 4, ploidy = c(2, 4))
        abs.cn <- absoluteCN(input.windows = windows, input.counts = counts, gc.params = gc.par)

        pdf("chrProfiles.pdf")
        chromosomeCNplots(abs.cn, y.max = 8)
        dev.off()

    ## End(Not run)

[Package Repitools version 1.26.0 Index]