CNV.detailplot: CNV.detailplot

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

Description

Create CNV plot for detail region.

Usage

CNV.detailplot(object, ...)

## S4 method for signature 'CNV.analysis'
CNV.detailplot(object, name, yaxt = "l",
  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).
name	character. Name of detail region to plot.
yaxt	character. Include y-axis? 'l': left, 'r': right, 'n': no. Defaults to 'l'.
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 detail regions CNV plots. Probes are shown as dots, bins 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.