README.Rmd

---
title: "rePROBE"
output: github_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

## Overview

Revised probe assignment and updated probe-set annotation in microarrays


## Installation

To install from GitHub:
```R
# install.packages("devtools")
devtools::install_github("friederhadlich/rePROBE")
```

## Usage

1. Prepare your microarray definition, genomic information and annotations using `ARG_LIST <- prepare_data()` to return a list of rePROBE arguments (ARG_LIST).
2. Perform the rePROBE - analysis using `run(ARG_LIST)`, which generates an appropiate environment object for the use with R packages i.e. [oligo](https://www.bioconductor.org/packages/release/bioc/html/oligo.html) or [affy](https://www.bioconductor.org/packages/3.8/bioc/html/affy.html).
3. Show a summarizing report using function `show_report(ARG_LIST)`.