SurprisalAnalysis R package guidelines

🖥️ Installation

To install the R package:

install.packages('devtools')
devtools::install_github('AnniceNajafi/SurprisalAnalysis')

Usage

To use the R package you should follow the steps below:

I. Store gene expression data in a csv file with the first row holding the sample names and the first column holding the gene names.
  1. Read the csv file and run the following code: 
  input.data <- read.csv('expression_data.csv')
  results <- surprisal_analysis(input.data)
  1. To run GO analysis on the patterns simply use the code below:

results[[2]]-> transcript_weights
percentile_GO <- 0.95 #change based on your preference
lambda_no <- 1 #change based on your preference
GO_analysis_surprisal_analysis(transcript_weights, percentile_GO, lambda_no, key_type = "SYMBOL", flip = FALSE, species.db.str =  "org.Hs.eg.db", top_GO_terms=15)

Use GUI from R package

Simply run the following code:

runSurprisalApp()

Web-based application

A web-based application based on the above has been deployed on this link.

Open source disclaimer

This is an open-source project based on a previously developed methodology. Requests or attempts on the expansion and further improvement of the code is welcome and encouraged.