EDIRquery

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, differ by at most a 1-bp mismatch, and 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

Example data provided includes a subset of the data for the gene GAA (ENSG00000171298) on chromosome 17.

To query the full the database, download the files at the link below, and provide the data directory to gene_lookup() in the path parameter.

Usage

Installation

To install this package, enter the following in R:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("EDIRquery")

Then load the package:

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
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

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.

Examples

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

# 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:

# 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:

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

Contact

Laura DT Vo Ngoc: doan.vongoc@vub.be