index.rmd

---
title: "LONGO: Long gene expression as a metric for neuronal identity"
author: "Alexander Paul, Matthew McCoy, Haijun Gong, Tae-Hyuk (Ted) Ahn,
Andrew Yoo"
date: "`r Sys.Date()`"
output:
    rmarkdown::html_vignette
    #word_document
vignette: >
    %\VignetteIndexEntry{Vignette Title}
    %\VignetteEngine{knitr::rmarkdown}
    %\VignetteEncoding{UTF-8}
---
## LONGO

LONGO is designed to have two different uses. One through a shiny interface
and another through R. Both of results of the program are
the same. The shiny interface will allow the user to alter certain variables
in the analysis to see how they will affect the result. This can be
useful when interpreting new data.

LONGO is designed to take in a data file with a gene identifier to get
the gene name and length. Occasionally there will be multiple probes going
to a single gene. LONGO can handle this in two different ways. The default way
is to get the mean expression values. The other option is to only keep the
probe that has the highest overall expression values. If a read has no
identified gene name or length in BioMart, the read is removed.

After getting the gene names and lengths the data is sorted by length. A
rolling window is used to create bins. The user can change the size of the
window as well as the step size of the window. These rolling window values
are then plotted. The P value plot shows the p value comparisons of the values
making up the windows to the window values in the control.