getPhiLogFC: Sample the log fold-change for each exon from a BMEA.MCMC...

In steveped/BMEA: Bayesian Modelling for Exon Arrays

Description

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

Usage

getPhiLogFC(data, contr.matrix, exonNames = NULL, 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 the simulations if kept.
exonNames	a character vector containing the exon (or group) names as specified on the cdf.
keepSims	a Boolean variable that determines whether the sampled values are returned in the output or just the summary statistics. Defaults to FALSE.

Details

Obtains the exon-specific posterior distribution for log fold-change for each supplied 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:

• summary a list with a separate component for each contrast. Each contrast-level component is a matrix with the summarised phi log fold-change for each exon within the transcript.

• sims a list with a separate component for each contrast. Each contrast-level component is a matrix of the sampled posterior disitributions for each contrast. Rows represent a kept iteration from the MCMC process, and columns represent each exon. Returns NULL if keepSims is set to FALSE.

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