exportTable-method: Methods for Function exportTable in Package 'CNAnorm'

In CNAnorm: A normalization method for Copy Number Aberration in cancer samples

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 [e-mail]

See Also

write.table

Examples

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

CNAnorm documentation built on Nov. 8, 2020, 5:29 p.m.