estimate_densities_modT: Estimate parameters under the null and alternative densities
In kjgleason/primo: Package in R for Integrative Multi-Omics association analysis

Description Usage Arguments Details Value

Estimate the parameters of the null and alternative density functions using moderated t-statistics.

1 2	estimate_densities_modT(betas, sds, df, alt_prop, mafs = NULL, N = NULL)

`betas`	vector of coefficient estimates.
`sds`	vector of standard errors (for coefficient estimates).
`df`	scalar or vector of first degrees of freedom of the F-distribution (usually, N-p-1).
`alt_prop`	proportion of test statistics from the alternative density.
`mafs`	vector of minor allele frequencies (MAFs) (optional). If `NULL`, no adjustment will be made for MAF in variance calculations.
`N`	scalar or vector of number of subjects (optional). Should be specified if `mafs!=NULL`.

Following Smyth (2004), the function calculates moderated t-statistics using conditional posterior means of the variance. The moderated t-statistics are used to estimate the null density under a t-distribution and the alternative density under a scaled t-distribution, each with moderated degrees of freedom.

A list with the following elements:

`Tstat_mod`	matrix of moderated t-statistics.
`df_mod`	vector of the moderated degrees of freedom.
`scaler`	vector of the scaling factors for the moderated t-statistics under the alternative.
`prior_df`	scalar of the prior degrees of freedom.
`prior_var`	scalar of the prior variance estimator.
`unscaled_var`	scalar of the unscaled variance prior on non-zero coefficients.