In CompEpigen/FactorViz: Visualization app for methylome decomposition experiments

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  collapse = TRUE,
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Introduction

The package provides an interactive visualization and reporting environment for exploring the results of the methylome decomposition experiments carried out by MeDeCom

Installation

You can install FactorViz through GitHub using devtools:

install.packages("devtools")
devtools::install_github("CompEpigen/FactorViz")

Using FactorViz

Default start-up

You can start FactorViz by using startFactorViz() command.

Parameterized start-up

You can also initialise FactorViz by providing paths to the files or the DecompPipeline output to the startFactorViz() command. It accepts the following parameters.

• decomp_output: takes in the directory path to DecompPipeline output
• medecom_set: takes in the path to medecom set file
• ann_C: takes in the path to CpG Annotation file
• ann_S: takes in the path to Sample Annotation file
• ref_meth: takes in the path to Reference Methylome file

Note: If decomp_output is provided all other parameters are force set to NULL

Loading Data-sets

Using DecompPipeline Output

If paramaters are not provided you can load the file by providing the path to DecompPipeline output directory (Fig 1a) in the user interface or by selecting the directory with the built-in file manager (Fig 1b, Fig 2)

Once selected you can check the file names of that will be loaded into FactorViz in the UI (Fig 3).

Using Multiple Files

With FactorViz you can also load the dataset from multiple location by switching the Non DeCompPipeline checkbox (Fig 4)

After the paths are set click on the Load Dataset button to load the dataset into FactorViz to carry out further analysis (Fig 5)

The further section of K Selection, Lambda Selection, LMC, Proportions and Meta-Analysis are explained in detail in MeDeCom documentation.

CompEpigen/FactorViz documentation built on April 30, 2020, 11:16 a.m.