glFrequency: Additional summary measured for the segments
Description
This program computes the frequency of gains and losses for each probe
as a function of level of mad.
Usage
glFrequency(xout, threshold=1)
Arguments
xout
an object of class DNAcopy
threshold
threshold value to call gain or loss
Value
A segment is called a gain or loss if the segment mean is at least the
threshold* mad distance away from the median copy number level. The
output is a data frame with five columns which give the chromosome
(chrom), genomic position (maploc), the number of samples with
available data (pfreq), and the gain (gain) and loss (loss).