estimateDeltaABBySmallDH.PairedPSCBS: Estimate a threshold for calling allelic balance from DH

In HenrikBengtsson/PSCBS: Analysis of Parent-Specific DNA Copy Numbers

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.
...	Not used.
verbose	See Verbose.

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.

Author(s)

Henrik Bengtsson

See Also

Instead of calling this method explicitly, it is recommended to use the *estimateDeltaAB() method.

HenrikBengtsson/PSCBS documentation built on Feb. 20, 2024, 9:01 p.m.