summary.adj: Summarize Laplace approximations

In bqtl: Bayesian QTL Mapping Toolkit

Summarize Laplace approximations

Description

The linear approximations of swap are much improved by the use a Laplace approximations for loci that are not markers. This function combines the results of a call like bqtl(y~configs(swap.obj),...) with the data in swap.obj to provide improved posteriors, et cetera

Usage

## S3 method for class 'adj'
summary(object, n.loc, coef.znames, mode.names=c("add",
"dom"), imp.denom=NULL, swap.obj=NULL,...)

Arguments

object	Typically, this is the result of a call like bqtl(y~configs(swap.obj),...)
n.loc	The number of genes in this model
coef.znames	map.names for the sample space
mode.names	NULL except for "F2", in which case it is uusally c("add","dom")
imp.denom	Optional, and only used when some sampling scheme other than the default MCMC generates object
swap.obj	The result of a call to swap
...	unused

Details

There are a lot of details. This sections nneds to be revised to reflect them.

Value

A list with components

adj	This multiplier adjusts the posterior odds for k vs k-1 gene models
var	An estimate of the variance of adj
coef	Posterior means of coefficients
loc	Marginal Posterior for location for k gene model
hk.ratio.mean	argh! I need to look this up

Author(s)

Charles C. Berry [e-mail]

References

Berry C.C. (1998) Computationally Efficient Bayesian QTL Mapping in Experimental Crosses. ASA Proceedings of the Biometrics Section, 164-169.

bqtl documentation built on Sept. 25, 2024, 1:08 a.m.