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Infinium Assay for Large-scale SNP Genotyping Applications
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A bedr way of genomic interval processing.

Syed Haider1, Daryl Waggott1, Emilie Lalonde1,2

  • 1Informatics and Biocomputing Platform, Ontario Institute for Cancer Research, Toronto, M5G 0A3 Canada.

Source Code for Biology and Medicine
|December 22, 2016
PubMed
Summary

The bedr R package offers a fast, robust interface for genomic interval manipulation, integrating command-line tools like BEDTools and BEDOPS directly into R pipelines for efficient data analysis and visualization.

Keywords:
BED formatData integrationGenomic intervalsSequence algebra

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Next-generation sequencing necessitates efficient genomic range handling in bioinformatics pipelines.
  • Common tasks include annotation, merging, and quantifying overlaps of genomic intervals.
  • Existing R packages often lack the speed or feature set of command-line tools like BEDTools.

Purpose of the Study:

  • To develop a robust R package for genomic coordinate manipulation.
  • To provide an R interface for established command-line tools (BEDTools, BEDOPS).
  • To facilitate rapid data handling and integration within R-based bioinformatics workflows.

Main Methods:

  • Developed the open-source R package 'bedr'.
  • Integrated BEDTools and BEDOPS as back-end engines for genomic interval operations.
  • Implemented functions for data manipulation, visualization, and database access (UCSC, COSMIC).

Main Results:

  • The bedr package enables rapid genomic interval data manipulation within R.
  • It creates R data structures compatible with existing computational pipelines.
  • Offers integrated data visualization and access to standard genomic databases.

Conclusions:

  • The bedr package provides an open-source solution for genomic interval data manipulation in R.
  • It enhances the capabilities of bioinformaticians and genomic researchers using R.
  • Facilitates efficient restructuring and analysis of genomic data within R programming language.