DexBatch-class: An S4 class for testing multiple compendia and/or parameters

Description Usage Details Methods (by generic) Slots

Description

The DexBatch class helps users test the effect of different parameter options and/or input compendia on gene module prediction.

Usage

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## Constructor:
dexBatch(compen, annmats, params = NULL, output = NULL)

## S4 method for signature 'DexBatch'
countJobs(object)

## S4 method for signature 'DexBatch'
runJob(object, j)

Details

A DexBatch object defines a set of jobs. Each job first predicts a set of gene modules, then evaluates their quality. Jobs within a DexBatch differ from each other in some way; the purpose of a DexBatch is to test the effect of these differences on the quality of the resulting modules.

Individual jobs in a DexBatch are executed by calling runJob. While each job could be run sequentially on a single machine, it is usually more practical when testing a large number of parameters to execude the jobs in parallel (see Use Cases in the DEXICA vignette)

If params is NULL, a single parameter set will be supplied using default values for the parameterSet constructor. If output is NULL, results will be directed to stdout().

Methods (by generic)

Slots

compen

A matrix or list of matrices containing the compendia to be tested

annmats

A matrix or list of matrices containing the annotation matrices to be used in module evaltation (see checkModules)

params

A ParameterSet object containing desired parameter ranges to be tested (see parameterSet)

output

Character string name of output file


MPCary/DEXICA documentation built on June 26, 2017, 7:35 p.m.