---
title: "EDIRquery"
author: "Laura D.T. Vo Ngoc"
date: "`r Sys.Date()`"
# output: rmarkdown::html_vignette
output: rmarkdown::pdf_document
sansfant: Calibri
vignette: >
  %\VignetteIndexEntry{EDIRquery}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)
```

# Introduction

Intragenic exonic deletions are known to contribute to genetic diseases and are 
often flanked by regions of homology. The Exome Database of Interspersed Repeats
(EDIR) was developed to provide an overview of the positions of repetitive 
structures within the human genome composed of interspersed repeats encompassing
a coding sequence. The package `EDIRquery` provides user-friendly tools to query
this database for genes of interest.



# Dataset

EDIR provides a dataset of pairwise repeat structures in which both sequences 
are located within a maximum of 1000 bp from each other, and fulfill one of the 
following selection criteria:

-   \>= 1 repeat located in an exon

-   Both repeats situated in different introns flanking one or more exons

A subset of EDIR is provided as example data, representing a subset of the 
interspersed repeats data for the gene GAA (ENSG00000171298) on chromosome 17.

<!-- To query the full the database, obtain the files at `(insert link here)` 
and provide the data directory to `gene_lookup()` in the `path` parameter. -->

To query the full the database, provide the data directory to `gene_lookup()` in
the `path` parameter.



# Usage

## Installation

To install this package, enter the following in R:

```{r, eval = FALSE}
if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EDIRquery")
```

Then load the package:

```{r, message = FALSE, warning = FALSE}
library("EDIRquery")
```

EDIR can easily be queried using the `gene_lookup` function, 
using the gene name and additional parameters:

| Argument | Description                                                                                                                                       | Default |
|----------------|---------------------------------------------|-----------|
| gene     | **required:** The gene name (ENSEMBLE ID or HGNC symbol)                                                                                          | \-      |
| length   | Repeat sequence length, must be between 7 and 20. If NA, results will include all available lengths in dataset for queried gene  | NA      |
| mindist  | Minimum spacer distance (bp) between repeats                                                                                                      | 0       |
| maxdist  | Maximum spacer distance (bp) between repeats                                                                                                      | 1000    |
| format  | Output table format. One of 'data.frame', 'GInteractions'.                                                                                                      | 'data.frame'    |
| summary  | Logical value indicating whether to store summary                                                                                                 | FALSE   |
| mismatch | Logical value indicating whether to allow 1 mismatch in sequence                                                                                  | TRUE    |
| path     | String containing path to directory holding downloaded dataset files. If not provided (`path = NA`), example subset of data will be used | NA      |



## Examples

A summary of the input printed to console, including the gene name, gene length 
(bp), Ensembl transcript ID, queried distance between repeats (default: 0-1000 
bp), and an overview of total results for the given repeat length. Console 
outputs include runtime.

Example querying the gene "GAA" with repeats of length 7, and allowing for 
1 mismatch:

```{r}
# Summary of results (printed to console)
gene_lookup("GAA", length = 7, mismatch = TRUE)
```

If no `length` is provided, a summary of all available repeat length results will
be printed:

```{r}
# Summary of results (printed to console)
gene_lookup("GAA", mismatch = TRUE)
```

Storing the output in a variable allows viewing of the individual results in the 
output dataframe:

```{r}
# Database output of query
results <- gene_lookup("GAA", length = 7, mismatch = TRUE)
head(results)
```

Changing the `format` parameter to `GInteractions` returns a GenomicInteractions 
object instead of a dataframe:

```{r}
# Database output of query
results <- gene_lookup("GAA", length = 7, format = "GInteractions", mismatch = TRUE)
head(results)
```


# Session info

```{r}
# Database output of query
sessionInfo()
```