CNV.write: CNV.write

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

Description

Output CNV analysis results as table.

Usage

CNV.write(object, ...)

## S4 method for signature 'CNV.analysis'
CNV.write(object, file = NULL, what = "segments")

Arguments

object	CNV.analysis object.
...	Additional parameters (CNV.write generic, currently not used).
file	Path where output file should be written to. Defaults to NULL: No file is written, table is returned as data.frame object.
what	character. This should be (an unambiguous abbreviation of) one of 'probes', 'bins', 'detail' or 'segments'. Defaults to 'segments'.

Value

if parameter file is not supplied, the table is returned as a data.frame object.

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.