dendRix: Run the MCMC sampler for dendRix.

In ttriche/dendRix: Port of DENDRIX (Vandin, Upfal, & Raphael, Genome Res, 2011) to R

Description

DE Novo DRIver eXclusivity... seek it out via MCMC sampling over mutation sets

Usage

dendRix(aberrations = NULL, K = 2, minFreq = 1, numIter = 999999, keep = 999, analyzed = NULL, stepLength = 999, c = 0.5)

Arguments

aberrations	A list, data.frame, or matrix (rows are subjects, columns are aberrations).
K	Cardinality of the sets to consider (should be deprecated soon).
minFreq	Minimum frequency to include an aberration (default is 1).
numIter	How many iterations to run the sampler for.
keep	How many of the top hits to retain.
analyzed	A list of aberrations to analyze (or NULL).
stepLength	How many steps to burn through between samples.
c	A constant.

Value

A list of the most visited (asymptotically, the weightiest) sets.

Author(s)

Tim Triche, Jr.

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

ttriche/dendRix documentation built on June 1, 2019, 2:50 a.m.