| name | bioconductor-rtracklayer |
| description | Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp |
| when_to_use | Use when: Genomic Track Import/Export: Importing and exporting genomic annotation tracks (e.g., BED, GFF, WIG) into R as GRanges objects using import and export.; UCSC Genome Browser Interaction: Interacting programmatically with the UCSC genome browser via browserSession.; Custom Track Uploads: Uploading custom annotation tracks to a genome browser using the track<- function.; UCSC Table Queries: Querying . Not for: For core manipulation of genomic intervals without file I/O, use GenomicRanges instead.; For parsing raw sequencing alignments, use GenomicAlignments or Rsamtools instead, as rtracklayer is designed for annotation tracks. |
| user-invocable | false |
rtracklayer
Dependencies & Environment
Package-intrinsic requirements from the Bioconductor landing page — reproduce in any R environment.
- Version: 1.72.0 · Bioconductor: 3.23 · R: ≥ 4.6
- Depends: GenomicRanges
- Imports: XML, BiocGenerics, S4Vectors, IRanges, XVector, Seqinfo, Biostrings, curl, httr, Rsamtools, GenomicAlignments, BiocIO, restfulr
- System requirements: URL
- Install:
BiocManager::install("rtracklayer")
When to Use
- Genomic Track Import/Export: Importing and exporting genomic annotation tracks (e.g., BED, GFF, WIG) into R as
GRanges objects using import and export.
- UCSC Genome Browser Interaction: Interacting programmatically with the UCSC genome browser via
browserSession.
- Custom Track Uploads: Uploading custom annotation tracks to a genome browser using the
track<- function.
- UCSC Table Queries: Querying and downloading built-in UCSC tracks (like RepeatMasker) using
ucscTableQuery and getTable.
When NOT to Use
- For core manipulation of genomic intervals without file I/O, use
GenomicRanges instead.
- For parsing raw sequencing alignments, use
GenomicAlignments or Rsamtools instead, as rtracklayer is designed for annotation tracks.
Data Requirements
- Input Formats: BED, GFF (v1/2/3), WIG, and other browser-supported formats.
- R Representation: Genomic coordinates must be 1-based when represented as
GRanges in R.
- Genome Build: Valid genome build identifiers (e.g., "hg18", "hg19") for UCSC integration.
Key Parameters
- format: Explicitly specifies the file format (e.g., "bed", "gff1") for
import or export.
- name: Character vector identifying the track within a
browserSession.
- range: A
GRanges object specifying the genomic segment to view or download.
- pack: Instructs the browser to use the "pack" mode for viewing a track.
- track: Specifies the name of the track to query in
ucscTableQuery.
- table: Specifies the specific table within a track to retrieve via
ucscTableQuery.
Best Practices
- Use
GRangesForUCSCGenome to formally associate interval data with a UCSC genome build and validate bounds before uploading.
- Subset large
GRanges tracks before uploading or viewing (e.g., targetTrack[1:10]) to avoid overwhelming the browser session.
- Rely on the default "auto" format detection in
export and import which derives the format from the file extension.
Common Pitfalls
- Coordinate System Confusion: R and
GRanges use 1-based coordinates, while formats like BED use 0-based. Fix: rtracklayer handles this automatically during import/export, so avoid manual coordinate shifting.
- Opening too many browser tabs: Changing the view state in UCSC opens a new page in the web browser. Fix: Consolidate view adjustments or use
browseGenome to load tracks and set the view in a single call.
Alternatives
- GenomicRanges: For in-memory manipulation of genomic intervals without external browser interaction.
- BSgenome: For retrieving and manipulating full genome sequences rather than annotation tracks.
Citations
- Lawrence M, et al. (2009) "Software for Computing and Annotating Genomic Ranges." PLoS Computational Biology.
- Lawrence M, et al. (2007) "rtracklayer: an R package for interfacing with genome browsers." Bioinformatics.
References
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