buildAppFile: Prepares a new network visualization

Description Usage Arguments

Description

This is the main function of the package, meant to prepare mutation data to be visualized by the discoverInteractiveAnalytics application.

Usage

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buildAppFile(mtdt, path_to_file, q.threshold = 0.01,
  mutation_effects = NULL, res.combined = NULL)

Arguments

mtdt

An indicator matrix, of the same type used in the DISCOVER test. The dimensions should be n genes (rows) by m columns (samples), with cells being 0 (non-mutated) or 1 (mutated).

path_to_file

Where to save the results. This file can be uploaded to the associated application.

q.threshold

The FDR cutoff used by the discover test, defaults to 0.01.

mutation_effects

Supply a list of mutations, with a column "gene" and "functionalEffect" to include mutation effects in the visualization. This is not necessary for the majority of functionality, therefore this function will run if it is not supplied.

network.name

The name of the network that will be displayed within the application.


connorH982/driverAnalytics documentation built on May 23, 2019, 8:55 a.m.