summary.fdr.bama {bama}

Summarize objects of type "fdr.bama"

Description

summary.fdr.bama summarizes the beta.m estimates from fdr.bama and for each mediator generates an overall estimate, credible interval, posterior inclusion probability (PIP), and PIP threshold for significance controlling for the specified false discovery rate (FDR).

Usage

## S3 method for class 'fdr.bama'
summary(
  object,
  rank = F,
  ci = c(0.025, 0.975),
  fdr = object$fdr,
  filter = T,
  ...
)

Arguments

object

An object of class "bama".

rank

Whether or not to rank the output by posterior inclusion probability. Default is TRUE.

ci

The credible interval to calculate. ci should be a length 2 numeric vector specifying the upper and lower bounds of the CI. By default, ci = c(0.025, .975).

fdr

False discovery rate. By default, it is set to whatever the fdr of object is. However, it can be changed to recalculate the PIP cutoff threshold.

filter

Whether or not to filter out mediators with PIP less than the PIP threshold.

...

Additional optional arguments to summary

Value

A data.frame with 4 elements. The beta.m estimates, the estimates' credible interval (which by default is 95\ inclusion probability (pip) of each 'beta.m'.