README.md

In vjcitn/amarettoTools: tools for working with AMARETTO outputs

title: "amarettoTools -- working with AMARETTO outputs" author: "Vincent J. Carey, stvjc at channing.harvard.edu" date: "r format(Sys.time(), '%B %d, %Y')" vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{amarettoTools -- working with AMARETTO outputs} %\VignetteEncoding{UTF-8} output: BiocStyle::html_document: highlight: pygments number_sections: yes theme: united toc: yes

Introduction

```{r setup,echo=FALSE,results="hide"} library(BiocStyle) library(amarettoTools)

AMARETTO is an integrative algorithm for identifying
driver genes in multiomic cancer studies.  In this
package we address the structure of AMARETTO results.

# An illustration in glioblastoma

The main result is a collection of modules of
coexpressed and coregulated genes.  The structure
of the collection can be captured in a graphNEL instance
as defined in the Bioconductor graph package.

```{r lklk}
library(amarettoTools)
data(regulGBM)
regulGBM
# how many modules
length(grep("Module", nodes(regulGBM)))
# target genes in Module_1
adj(regulGBM, "Module_1")
# regulators of Module_1
inEdges("Module_1", regulGBM)
# weights for regulators of module 1
m1regs = inEdges("Module_1", regulGBM)[[1]]
t(t(sapply(edgeWeights(regulGBM, m1regs), "[", "Module_1")))

Conclusions

This graph losslessly collects the relationship information in the AMARETTO run. The expression data are propagated but as far as I can tell, they are just the expression quantifications from firehose? So they should not be propagated but queried from the original source.

vjcitn/amarettoTools documentation built on May 20, 2019, 12:32 p.m.