CompGenomics-metaGEO

Quickstart guide

Following this guide will build an example metaGEO app comparing multiple psoriasis studies. More details on how to create a new metaGEO can be found by following the vignette.

Clone this repository

git clone https://github.com/AbbVie-ComputationalGenomics/metaGEO.git

Start an Rstudio session

R package requirements

To install all dependencies run:

source("https://bioconductor.org/biocLite.R")
  biocLite(c('shiny',
          'shinyjs',
          'shinyBS',
          'lattice',
          'logging',
          'hgu133plus2.db',
          'org.Hs.eg.db', 
          'knitr',
          'gdata',
          'dbConnect',
          'RSQLite',
          'GEOmetadb',
          'xtable',
          'rmarkdown',
          'devtools',
          'reshape2'))

Pandoc requirement

Please install the appropriate system build of Pandoc

https://github.com/jgm/pandoc/releases/tag/1.19.2.1

General process flow

Download full-size .PDF

Run the psoriasis vignette

setwd('metaGEO/vignettes')

Perform the initial rendering (May take a few minutes depending on network speed):

library(rmarkdown)
render('build_metageo_instance.Rmd')

Upon successful rendering, load the resulting build_metageo_instance.html file in your browser.

Run example metaGEO shiny-app

Copy or move the .Rdata file generated from the vignette to the shiny app's data location:

file.rename('ObjectWithGeoData_psoriasis.Rdata', '../inst/shiny-examples/data/ObjectWithGeoData_psoriasis.Rdata')
setwd('../inst/shiny-examples/')

Start the app

library(shiny)
runApp("metaGEO")