getLogFC: Sample the log fold-change from a BMEA.MCMC dataset

In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description

Samples the posterior distribution of log fold-change for each specified contrast from the given dataset.

Usage

getLogFC(data, contr.matrix, keepSims = FALSE)

Arguments

data	an object of class BMEA.MCMC. Will contain a set of simulations for every condition-specific expression level.
contr.matrix	a contrast matrix with rows representing each condition & columns representing the specific contrasts. The column names are recycled as rownames in the summary output & for thesimulations if kept.
keepSims	logical variable. Determines whether the sampled values are returned in the output or just the summary statistics. Defaults to FALSE.

Details

Obtains the posterior distribution for log fold-change for each contrast by direct sampling from the MCMC output. A summary for each contrast with mean, sd & the quantiles are returned in the $summary argument as the default.

All data is retrieved using C and this function is a simple wrapper to the C function.

Value

A list with the following components:

• summarya summary matrix with mean, standard deviation and the quantiles for each contrast. Each row represents a different contrast.

• simsa matrix of the sampled posterior disitributions for each contrast. Rows represent a kept iteration from the MCMC process, and columns represent each contrast. Returns NULL if keepSims is set to FALSE

steveped/BMEA documentation built on May 30, 2019, 5:38 p.m.