CNV.detailplot {conumee}R Documentation

CNV.detailplot

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 conumee@hovestadt.bio

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')
[Package conumee version 1.13.0 Index]