copyCountSegments:
Segments of identical copy count from exomeCopy
Description
Unpacks an ExomeCopy object and returns a RangedData object with
segments of identical predicted copy count in genomic coordinates.
Usage
copyCountSegments(object)
Arguments
object
ExomeCopy object
Value
Returns a RangedData object with the predicted copy count, the log
odds of predicted copy count over normal copy count, a combined
p-value, the number of genomic ranges spanned by the segment, the
number of targeted basepairs in the segment, and the sample name.
Details
The log odds column is calculated by summing the log ratios over the
contained ranges. The log ratios at each range is the log of the
emission probability for the given read count for the predicted state
divided by the emission probability for the normal state. The higher
the value, the more likely that the read counts in this range could
not have been generated from the normal state.