CNV.genomeplot: CNV.genomeplot

In conumee: Enhanced copy-number variation analysis using Illumina DNA methylation arrays

Description

Create CNV plot for the whole genome or chromosomes.

Usage

CNV.genomeplot(object, ...)

## S4 method for signature 'CNV.analysis'
CNV.genomeplot(object, chr = "all", chrX = TRUE,
  chrY = TRUE, centromere = TRUE, detail = TRUE, main = NULL,
  ylim = c(-1.25, 1.25), set_par = TRUE, cols = c("red", "red",
  "lightgrey", "green", "green"))

Arguments

object	CNV.analysis object.
...	Additional parameters (CNV.detailplot generic, currently not used).
chr	character vector. Which chromomsomes to plot. Defaults to 'all'.
chrX	logical. Plot values for chrX? Defaults to TRUE. Set CNV.create_anno(chrXY = FALSE) if chrX and Y should not be included at all.
chrY	logical. Plot values for chrY? Defaults to TRUE.
centromere	logical. Show dashed lines at centromeres? Defaults to TRUE.
detail	logical. If available, include labels of detail regions? Defaults to TRUE.
main	character. Title of the plot. Defaults to sample name.
ylim	numeric vector. The y limits of the plot. Defaults to c(-1.25, 1.25).
set_par	logical. Use recommended graphical parameters for oma and mar? Defaults to TRUE. Original parameters are restored afterwards.
cols	character vector. Colors to use for plotting intensity levels of bins. Centered around 0. Defaults to c('red', 'red', 'lightgrey', 'green', 'green').

Details

This method provides the functionality for generating CNV plots for the whole genome or defined chromosomes. Bins are shown as dots, segments are shown as lines. See parameters for more information.

Value

NULL.

Author(s)

Volker Hovestadt [e-mail]

Examples

# prepare
library(minfiData)
data(MsetEx)
d <- CNV.load(MsetEx)
data(detail_regions)
anno <- CNV.create_anno(detail_regions = detail_regions)

# create/modify object
x <- CNV.segment(CNV.detail(CNV.bin(CNV.fit(query = d['GroupB_1'],
    ref = d[c('GroupA_1', 'GroupA_2', 'GroupA_3')], anno))))

# output plots
CNV.genomeplot(x)
CNV.genomeplot(x, chr = 'chr6')
CNV.detailplot(x, name = 'PTEN')
CNV.detailplot_wrap(x)

# output text files
CNV.write(x, what = 'segments')
CNV.write(x, what = 'detail')
CNV.write(x, what = 'bins')
CNV.write(x, what = 'probes')

conumee documentation built on Nov. 8, 2020, 6 p.m.