update_allelic_number: Update allelic number (and, of course, configuration, too) in...

In fboehm/reducedscan: QTL Scans with Simpler Statistical Models in Multiparental Populations

Description

Update allelic number (and, of course, configuration, too) in Jannink and Wu 2003 MCMC.

Usage

update_allelic_number(
  configuration,
  genoprobs,
  effects,
  trait,
  residual_variance,
  prior,
  poisson_prior_mean = 2
)

Arguments

configuration	an allelic series matrix, ie, binary matrix of 0s and 1s mapping founders to alleles at a single QTL
genoprobs	genotype probabilities matrix for a single marker, ie, n_subjects by n_founders at 1 marker
effects	vector containing current value of allelic effects, one entry per allele
trait	a univariate trait matrix, n by 1
residual_variance	residual variance
prior	takes values "poisson" or "uniform" to specify which prior to use.
poisson_prior_mean	Lambda, mean value, for the untruncated Poisson distribution

Details

If a poisson prior is used for the allelic number, it is truncated to 2, 3, ..., number of founders (8 in the case of Diversity Outbred mice).

fboehm/reducedscan documentation built on April 30, 2021, 8:31 p.m.