calc.priors: Calculate prior probability of being a risk SNP

In aaronwolen/bingd: Bayesian integration of genomic data

Description

Calculate prior probability of being a risk SNP

Usage

calc.priors(object, effect = 2, adjust = NULL, verbose = FALSE,
  trace = 0)

## S4 method for signature 'GWAS'
calc.priors(object, effect = 2, adjust = NULL,
  verbose = FALSE, trace = 0)

Arguments

object	AnnotatedGWAS object
effect	assumed effect size, used to shift the ideal z-score distribution
adjust	optional parameter to adjust P(R) for linkage disequilibrium
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.

Value

A list with components:

p.r

P(R): prior probability of being a risk SNP

p.n

P(N): prior probability of a SNP having no effect

lambda

GWAS inflation factor (λ)

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