Repitools (version 1.18.0)

chromosomeCNplots: 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

"chromosomeCNplots"(copy, y.max = NULL, pch = 19, cex = 0.2, pch.col = "black", seg.col = "red", lty = 1, lwd = 2, verbose = TRUE) "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.

Value

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

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.

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)