exportTable {CNAnorm} | R Documentation

## Methods for Function exportTable in Package ‘CNAnorm’

### Description

`exportTable` write a table with normalised values of each window. A wrapper to `"write.table"`

### Usage

    ## S4 method for signature 'CNAnorm'
    exportTable(object, file = "CNAnorm_table.tab", show = 'ratio',
        sep = "\t", row.names = FALSE, ...)

### Arguments

`object` | an object of Class `"CNAnorm"`
`file` | name of the file to save to
`show` | what should be reported in the table: `"ratio"`: the normalized ratio (a value of 1 means diploid). `"ploidy"`: the same as ratio * 2. `"center"`: report ratio centered on the most abbundant copy. Ratio of 1 means that the most abbundant “state” is centered to 1
`sep` | the field separator string.
`row.names` | either a logical value indicating whether the row number should be written or a character vector of row names to be written.
`...` | Extra arguments to be passed to `"write.table"`

### Details

It produces a tab delimited text file with the following columns:

Chr: Chromosome/contig name.

Pos: Starting position of the window.

Ratio: Ratio Test/Normal for each window after GC correction.

Ratio.n: Ratio Test/Normal or ploidy for each window after normalisation.

Ratio.s.n: Smoothed and normalised ratio Test/Normal or ploidy for each window.

SegMean: Mean of the segment this window belongs to.

SegMean.n: Normalised mean ratio Test/Normal or ploidy of the segment this window belongs to.

### Value

An object of class `"CNAnorm"`

### Author(s)

Stefano Berri s.berri@leeds.ac.uk

### See Also

`write.table`

### Examples

    data(CN)
    CN <- validation(CN)
    CN <- discreteNorm(CN)
    exportTable(CN, file = "CNAnorm_table.tab", show = 'ploidy')

[Package CNAnorm version 1.38.0 Index]