subset_Primo_obj: Subset a Primo object.

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

Description

Subset results from Primo output based on a vector of indices.

Usage

subset_Primo_obj(Primo_obj, idx)

Arguments

Primo_obj	list of results returned by Primo (from the function Primo_tstat, Primo_pval, Primo_modT or Primo_chiMix).
idx	integer vector of the indices to subset Primo results.

Value

A list of Primo results with the following elements:

post_prob	matrix of posterior probabilities (each column corresponds to an association pattern).
pis	vector of estimated proportion of SNPs belonging to each association pattern.
D_mat	matrix of densities under each association pattern.
Gamma	correlation matrix.

• If the results were originally from the t-statistic version, the list will additionally contain:

  Tstat_mod	matrix of moderated t-statistics.
  V_mat	matrix of scaling factors under the alternative distribution.
  mdf_sd_mat	matrix of standard deviation adjustment according to moderated degrees of freedom: sqrt(df/(df-2)).
  prior_df	vector of the prior degrees of freedom for each marginal distribution.
  prior_var	vector of the prior variance estimators for each marginal distribution.
  unscaled_var	vector of the unscaled variance priors on non-zero coefficients for each marginal distribution.

• If the results were originally from the P-value version, the list will additionally contain:

  chi_mix	matrix of -2*log(P)-values.
  A	vector of scaling factors under the alternative densities.
  df_alt	vector of degrees of freedom approximated for the alternative densities.

kjgleason/primo documentation built on Sept. 7, 2021, 5:21 p.m.