chromosomeCNplots: Plot copy number by chromosome

In Repitools: Epigenomic tools

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)

Repitools documentation built on Nov. 8, 2020, 7:52 p.m.