In taylorpourtaheri/nr: Node prioritization optimizer

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

noderank

noderank maps differential gene expression results onto an established network of protein-protein associations and employs network analysis methods to select a prioritized list of important nodes. For data in which the mechanism of perturbation is known, each ranked list result is scored by the position of the causal gene.

Installation

You can install the released version of noderank from GitHub with:

devtools::install_github("hemoshear/noderank")

A roadmap for noderank:

Input: Differential gene expression analysis results including log fold-changes and p-values, i.e. the output of topTable() from limma or results() from DESeq2.

1. Generate protein-protein interaction network.
2. Map DEA results onto the PPI.
3. Prune the network by user-specified thresholds for fold-change and p-value.
4. Implement user-specified network analysis algorithm to rank the nodes of the network.
5. Calculate overall network score and uncertainty metrics.

Output:

• The final network composed of the important genes.

• A dataframe of important genes with their associated ranking metrics.

• The mean score and p-value for the overall network.

taylorpourtaheri/nr documentation built on Dec. 23, 2021, 7:49 a.m.