README.md

In rmflight/black_mirna_mrna_nsclc_network_enrichment: Network Analysis for Penni Black Data

black.miRNAmRNA.NSCLC.networkEnrichment

This R package contains functions and a vignette describing the generation of a STRING based protein-protein interaction (PPI) network for miRNA and mRNA data for NSCLC cells for the publication:

W Wu, RM Flight, MJ Krentz, B Kulengowski, H-F Li, HNB Moseley, A Stromberg and EP Black, Interacting miRNA and mRNA genes identify potential therapeutic targets for NSCLC, sumbitted Feb 2015

Installation

If you want to be able to install this package directly and use it without modification to the vignette, then you are best doing a clone and then install using devtools, as the STRING database files are installed in inst/extdata/STRING so that there is no confusion about their location.

git clone https://github.com/rmflight/black_mirna_mrna_nsclc_network_enrichment.git
cd black_mirna_mrna_nsclc_network_enrichment/inst/extdata/STRING
wget http://string-db.org/newstring_download/protein.links.detailed.v9.1/9606.protein.links.detailed.v9.1.txt.gz
wget http://string.uzh.ch/permanent/string/9_1/protein_aliases/9606__protein_aliases_tf.tsv.gz

cd ../../../..
R CMD INSTALL black_mirna_mrna_nsclc_network_enrichment

To run the enrichment vignette, you will also need to install the following packages:

in R

library(BiocInstaller)
biocLite(c("graph", "org.Hs.eg.db", "hgu133plus2.db", "GO.db"))

If you want to re-generate the network figure, you will also need to install Cytoscape 2.8 with the CytoscapeRPC plugin, and the RCytoscape Bioconductor package:

biocLite("RCytoscape")

Original Output

All of the original tables and figures generated for the manuscript are in the inst/extdata/output directory

Re-running Vignettes

If you want to re-run the vignettes for the network generation and enrichment, you can generate them all by using:

library(devtools)
build_vignettes()

Alternatively, you can use knitr directly:

library(knitr)
knit("vignettes/networkAnalysis.Rmd")
knit("vignettes/figureGeneration.Rmd")

License

Licensed under the MIT License. This software is provided as-is, with no implied warranty.

rmflight/black_mirna_mrna_nsclc_network_enrichment documentation built on May 27, 2019, 9:30 a.m.