README.md

In vjcitn/AmObjects: Object design (S4) for AMARETTO

title: "AmObjects: Systematic data structures for AMARETTO" author: "AMARETTO team" date: "r format(Sys.time(), '%B %d, %Y')" vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{AMARETTO S4 Object Design Considerations} %\VignetteEncoding{UTF-8} output: BiocStyle::html_document: highlight: pygments number_sections: yes theme: united toc: yes

Introduction

The general problem of multiomic data integration leads to unusual situations of data volume, complexity, and annotation. Metrics for comparing solutions are not readily available.

In the AmObjects package we use R's S4 object design disciplines to hide complexity from end-users and to provide hints so that model setup and results are easily used in workflows that will evolve over time.

Initializing the AMARETTO procedures

In the following, iniobj is a lossless representation of the TCGA-LIHC_AMARETTOinit constructed as a small test case. ```{r chk1} library(AmObjects) origlist = AmObjects::LIHC_AMARETTOinit names(origlist) iniobj = AmInit(origlist) iniobj

# Representing AMARETTO results

```{r chk2}
reslist = AmObjects::LIHC_AMARETTOresults
names(reslist)
resobj = AmResults(reslist)
resobj

vjcitn/AmObjects documentation built on May 12, 2019, 12:29 a.m.