copyCountSegments: Segments of identical copy count from exomeCopy

In exomeCopy: Copy number variant detection from exome sequencing read depth

Description

Unpacks an ExomeCopy object and returns a GRanges object with segments of identical predicted copy count in genomic coordinates.

Usage

  copyCountSegments(object)

Arguments

object

ExomeCopy object

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.

Value

Returns a GRanges 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.

See Also

exomeCopy ExomeCopy-class

Examples

example(exomeCopy)
copyCountSegments(fit)

exomeCopy documentation built on Nov. 8, 2020, 7:45 p.m.