CNAnorm (version 1.18.0)

exportTable: Methods for Function exportTable in Package `CNAnorm'

Description

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

Usage

"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"

Value

"CNAnorm"

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.

See Also

write.table

Examples

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