GetLLRAge: LLR-age from Ageprior Matrix
In sequoia: Pedigree Inference from SNPs

GetLLRAge

R Documentation

LLR-age from Ageprior Matrix

Description

Get log10-likelihood ratios for a specific age difference from matrix AgePriorExtra.

Usage

GetLLRAge(AgePriorExtra, agedif, patmat)

Arguments

`AgePriorExtra`	matrix in `sequoia` output
`agedif`	vector with age differences, in whole numbers. Must occur in rownames of `AgePriorExtra`.
`patmat`	numeric vector; choose maternal (1), paternal (2) relatives, or for each relationship the most-likely alternative (3).

Details

This is a simple helper function to extract values from AgePriorExtra, e.g. to use together with CalcPairLL.

Value

A matrix with nrow equal to the length of agedif, and 7 columns: PO-FS-HS-GP-FA-HA-U.

Examples

# For a pair with unknown age difference, explore the difference age-based
# LLRs for all relationships, for a range of plausible age differences.
PairsG <- data.frame(ID1 = 'A', ID2 = 'B', AgeDif = rep(c(-2,2,3),2),
                   PatMat = rep(1:2, each=3))
cbind(PairsG,
      GetLLRAge(SeqOUT_griffin$AgePriorExtra,
                agedif = PairsG$AgeDif, patmat = PairsG$PatMat))

sequoia documentation built on Aug. 21, 2025, 5:43 p.m.