getNTAI.raw: Compute the number of non-telomeric allelic imbalance (NTAI)...

In maxwell-lab/HRDex:

Description

Compute the number of non-telomeric allelic imbalance (NTAI) events

Usage

getNTAI.raw(seq.dat, min.seg.size = 1.1e+07)

Arguments

seq.dat	the data.frame of sequencing data
min.seg.size	the minimum segment size

Details

raw NTAI is calculated as the number of segments where the segment size is greater than the minimum segment size; allelic imbalance is present; the segment does not cross the centromere; and the segment is not in either of the telomeres.

Value

the number of NTAI events

Examples

seq.dat <- preprocessHRD( seq.dat )
CN.dat <- getCNt( seq.dat )

## the number of NTAI events in seq.dat
ntai <- getNTAI.raw( seq.dat )

maxwell-lab/HRDex documentation built on May 3, 2020, 9:01 p.m.