exportTable {CNAnorm} | R Documentation |
exportTable
write a table with normalised values of each window. A wrapper to "write.table"
## S4 method for signature 'CNAnorm' exportTable(object, file = "CNAnorm_table.tab", show = 'ratio', sep = "\t", row.names = FALSE, ...)
object |
an object of Class |
file |
name of the file to save to |
show |
what should be reported in the table: |
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 |
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.
An object of class "CNAnorm"
Stefano Berri s.berri@leeds.ac.uk
data(CN) CN <- validation(CN) CN <- discreteNorm(CN) exportTable(CN, file = "CNAnorm_table.tab", show = 'ploidy')