conumee (version 1.4.2)

CNV.detailplot_wrap: CNV.detailplot_wrap

Description

Create CNV plot for all detail regions.

Usage

CNV.detailplot_wrap(object, ...)
"CNV.detailplot_wrap"(object, set_par = TRUE, main = NULL, ...)

Arguments

object

CNV.analysis object.

...

Additional paramters supplied to CNV.detailplot.

set_par

logical. Use recommended graphical parameters for oma and mar? Defaults to TRUE. Original parameters are restored afterwards.

main

character. Title of the plot. Defaults to sample name.

Value

NULL.

Details

This method is a wrapper of the CNV.detailplot method to plot all detail regions.

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')