Primo_modT: Estimate posterior probabilities of association patterns,...
In kjgleason/primo: Package in R for Integrative Multi-Omics association analysis

Description Usage Arguments Details Value

For each observation (e.g. SNP), estimates the posterior probability of each association pattern. This version of the main Primo function uses moderated t-statistics and parameters previously calculated under the 'limma' framework (i.e. using estimate_densities_modT). It is useful for cases where the same statistic from one study (e.g. gene-SNP pair) may be mapped to multiple statistics from another study (e.g. multiple gene-CpG pairings). Utilizes parallel computing, when available.

1	Primo_modT(Tstat_mod, mdfs, V_mat, Gamma, tol = 0.001, par_size = 1)

`Tstat_mod`	matrix of moderated t-statistics.
`mdfs`	matrix of moderated degrees of freedom.
`V_mat`	matrix of scaling factors.
`Gamma`	correlation matrix.
`tol`	numeric value specifying the tolerance threshold for convergence.
`par_size`	numeric value specifying the number of workers for parallel computing (1 for sequential processing).

The following are additional details describing the input arguments (for m SNPs/observations measured in d studies):

`Tstat_mod`	m x d matrix.
`mdfs`	m x d matrix.
`V_mat`	m x d matrix.
`Gamma`	d x d matrix.

A list with the following elements:

`post_prob`	matrix of posterior probabilities (each column corresponds to an association pattern).
`pis`	vector of estimated proportion of observations belonging to each association pattern.
`D_mat`	matrix of densities under each association pattern.
`Gamma`	correlation matrix.
`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: df/(df-2).

The main element of interest for inference is the posterior probabilities matrix, post_prob. The estimated proportion of observations belonging to each association pattern, pis, may also be of interest. The remaining elements are returned primarily for use by other functions.

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