estimateDeltaABBySmallDH.PairedPSCBS: Estimate a threshold for calling allelic balance from DH
Description
Estimate a threshold for calling allelic balance from DH.Usage
## S3 method for class 'PairedPSCBS':
estimateDeltaABBySmallDH(fit, q1=0.05, q2=0.9, ..., verbose=FALSE)
Arguments
q1
A numeric value specifying the weighted quantile of the
segment-level DHs used to identify segments with small DH means. q2
A numeric value specifying the quantile of the locus-level
DH signals for those segments with small DH mean levels. Value
- Returns the threshold estimate as a
numeric scalar.
Algorithm
- Grabs the segment-level DH estimates.
- Calculate segment weights proportional to the number
of heterozygous SNPs.
- Calculate$\Delta$as the 5\% quantile of the weighted DH means.
- Choose the segments with means less than$\Delta$.
- Calculate threshold$\Delta_{AB}$as the 90\% "symmetric" quantile
of the observed locus-level DHs from the selected segments
in Step 4.
The q:th "symmetric" quantile is estimated by estimating
the ((1-q), 50\%) quantiles, calculating their distance as
"50\%-(1-q)" and add to the median (50\%), i.e.
"median + (median-(1-q))" = "2*median-1 + q", which should
equal q if the distribution is symmetric.
See Also
Instead of calling this method explicitly, it is recommended
to use the *estimateDeltaAB() method.