calc.bayes: Calculate posterior probability of being an effective SNP

In aaronwolen/bingd: Bayesian integration of genomic data

Description

Integrate GWAS results with annotated genomic features

Usage

calc.bayes(object, risk.thresh = NULL, adjust = NULL, effect = 2,
  prob.risk = NULL, verbose = FALSE, trace = 0)

## S4 method for signature 'AnnotatedGWAS'
calc.bayes(object, risk.thresh = NULL,
  adjust = NULL, effect = 2, prob.risk = NULL, verbose = FALSE,
  trace = 0)

Arguments

object	AnnotatedGWAS object
risk.thresh	the p-value threshold applied to identify “risky” markers
adjust	optional parameter to adjust P(R), as well as conditional probabilities for linkage disequilibrium
effect	assumed effect size, used to shift the ideal z-score distribution
prob.risk	probability of being a risk SNP, this is normally calculated automatically but can be supplied in situations where the result was 0
verbose	print out intermediate statistics calculated during the analysis
trace	Non-negative integer. If positive, tracing information on the progress of the optimization is produced. See optim for details.

aaronwolen/bingd documentation built on May 10, 2019, 4:04 a.m.