https://github.com/vjcitn/amarettotools
software for organizing AMARETTO results
https://github.com/vjcitn/amarettotools
Last synced: 4 months ago
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software for organizing AMARETTO results
- Host: GitHub
- URL: https://github.com/vjcitn/amarettotools
- Owner: vjcitn
- Created: 2018-08-09T13:53:58.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2018-08-09T16:07:08.000Z (almost 7 years ago)
- Last Synced: 2025-01-09T13:46:11.722Z (5 months ago)
- Language: R
- Size: 432 KB
- Stars: 0
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
---
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.