Primo_conditional: Perform conditional analysis for a specified variant.

In kjgleason/Primo: Package in R for Integrative Multi-Omics association analysis

Description

For a specified variant, re-estimate the posterior probabilities of association patterns, conditioning on other specified variants (e.g. lead SNPs for omics traits). Returns the association pattern with the highest posterior probability after conditional analysis.

Usage

Primo_conditional(idx_snp, idx_leadsnps, LD_mat, Primo_obj)

Arguments

idx_snp	integer matching the index (e.g. row of Tstat_mod) of the genetic variant for which to perform conditional analysis.
idx_leadsnps	vector of indices (e.g. rows of Tstat_mod) of the leading snps on which to condition.
LD_mat	matrix of genotype correlation coefficients (e.g. Pearson r). Rows and columns should match the order of (idx_snp, idx_leadsnps).
Primo_obj	list returned by running the t-statistic version of Primo (i.e. Primo_tstat or Primo_modT)

Value

The integer corresponding to the association pattern with the highest posterior probability following conditional analysis. The value returned, k, corresponds to the k-th index of pis from the Primo output, and the k-th row of the Q matrix produced by make_qmat.

kjgleason/Primo documentation built on Sept. 7, 2021, 3:58 a.m.