Working with genomics ranges
Last updated on 2024-11-19 | Edit this page
Overview
Questions
- What is the recommended way to represent coordinates on a genomic scale in Bioconductor?
- What Bioconductor packages provides methods to efficiently process genomic ranges?
- How can I import/export sets of genomic coordinates from/to various genomic file formats?
Objectives
- Explain how genomic coordinates and intervals are represented in the Bioconductor project.
- Identify Bioconductor packages and methods available to process ranges of genomic coordinates.
Install packages
Before we can proceed into the following sections, we install some
Bioconductor packages that we will need. First, we check that the BiocManager
package is installed before trying to use it; otherwise we install it.
Then we use the BiocManager::install() function to install
the necessary packages.
R
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GenomicRanges")
The GenomicRanges package and classes
Why do we need classes for genomic ranges?
In the era of genomics, many observations are reported as ranges of coordinates - i.e., intervals - on a genomic scale. Depending on the nature of the assay, those genomic ranges may represent genes, transcripts, exons, single nucleotide polymorphisms (SNPs), transcription factor binding sites, or peaks from next-generation sequencing assays such as ChIP-seq or ATAC-seq.
Genomic ranges tie those observations of assayed values (e.g., gene expression) to a physical location in the genome or an organism. For instance, those genomic ranges can be used to query physical proximity or overlap between assayed features and databases of known regulatory regions.
Often, the final genomic ranges used for reporting measurements are the result of combinations and operations on sets of genomic ranges in databases of known genomic features. For instance, in RNA-sequencing, next-generation sequencing reads are often counted within individual exons, and those counts are subsequently aggregated across all the exons of each gene. Separately, promoters are frequently defined as region of arbitrary width, partly upstream and/or downstream of known transcription start sites (TSS).
Importantly, genomic ranges do not necessarily need to span multiple coordinates. The notion of range is meant in the mathematical way, and single-nucleotide genomic ranges (e.g., SNPs) can be described as opening and closing at the same coordinate (or at the next coordinate, in the case of a right-open interval).
For many organisms, the genetic material is split into a number of separate nucleic acid molecules (e.g., chromosomes, plasmids). As such, genomic ranges are described by the name of the sequence and the numeric interval of coordinates on that sequence.
Example uses of the GenomicRanges algebra. Adapted from Huber, Carey, Gentleman, Anders, Carlson, Carvalho, Bravo, Davis, Gatto, Girke, Gottardo, Hahne, Hansen, Irizarry, Lawrence, Love, MacDonald, Obenchain, Oles, Pages, Reyes, Shannon, Smyth, Tenenbaum, Waldron, and Morgan (2015). The figure illustrates the example of a gene model that comprises two transcripts, and the definition of various genomic ranges relative to that gene model. For instance - in this specific illustration - unspliced transcripts summarise the entire range of coordinates from the start of the first exon to the end of the last exon; while the gene region is defined as the set of coordinates included in at least one exon of one transcript.
A brief introduction to intervals
Intervals are described in mathematical terms using a start and an end position on an axis of continuous coordinates. The interval then comprises all the real numbers between those two coordinates, and the width of each interval can be computed from the difference between the coordinates of the start and end positions.
Generally speaking, the start and end position can be any rational number, including floating-point numbers. However, in genomics, integer coordinates are typically used to represent the location of monomers (e.g., nucleotide, amino acid) in the sequence of polymers (e.g., nucleic acid, protein).
You may come across packages, databases, and programming languages that use different rules to define intervals. In R, indexing is 1-based (meaning that the first position in a sequence is 1), which contrasts with Python that is 0-based (the index of the first position in a sequence is 0). Similarly, references files in the UCSC Genome Browser are 0-based, while those of the Ensembl Genome Browser are 1-based.
The definition of intervals in a shared coordinate system allows calculations such as the distance between two intervals - generally calculated as the distance between the two closest edges of those intervals -, and the identification of overlapping intervals.
Example of intervals. Three intervals named A, B, and C, are represented. Interval A starts at position 5 and ends at position 9, for a width of 4 units; interval B starts at position 1 and ends at position 3, for a width of 2 units; interval C starts at position 3 and ends at position 6, for a width of 3 units. Intervals A and C overlap, from coordinates 5 to 6; while intervals B and C meet at coordinate 3, but do not strictly overlap each other.
A brief introduction to genomic ranges
Genomic ranges essentially extend the notion of mathematical intervals on sets of biological sequences (e.g., chromosomes). In other words, genomic ranges combine the name of the biological sequence on which they are located with the integer range of coordinates that the genomic ranges span in that sequence. This is key to distinguish genomic features that span an overlapping range of coordinates on different biological sequences.
Furthermore, the double-stranded nature of DNA sequences also adds the notion of strandedness to genomic ranges. If known, the strand information of genomic features is a key piece of information that should be tracked, so that it may be used for downstream analyses. For instance, genomic ranges spanning a common range of coordinates on opposite strands of the same DNA sequence may not be considered to overlap (e.g., for the purpose of strand-specific next-generation sequencing assays).
Genomic ranges are closed intervals - the start and end positions are included in the interval; in the example of nucleic acids, the start position indicates the first nucleotide in the interval, and the end position indicates the last nucleotide in the interval.
Example of genomic ranges. Genomic ranges are defined by the name of the biological sequence in which they are located (here, “chr1”), and the positions of start and end in that sequence. Here, numeric positions are not explicitly shown, but implied by the sequence of nucleic acids and the arrow indicating coordinates increasing from the left to the right. In this example, genomic ranges can be used to describe individual exons, with metadata grouping those exons into transcripts and genes. Furthermore, the strandedness of exons, transcripts, and genes is an important piece of information to precisely describe the location of each genomic range in the double-stranded DNA polymer.
The GenomicRanges package
Overview
The GenomicRanges package implements S4 classes to represent genomic ranges as S4 objects.
Specifically, the GRanges class is designed to store a
set of intervals including the name of the sequence where features are
located as well as the range of integer coordinates spanned by the
feature in that sequence.
More generally, the IRanges class is designed to store a
set of intervals over a range of integer coordinates, without the notion
of sequence names. As such, a GRanges object is merely the
combination of an IRanges object and a vector of sequence
names.
Those S4 classes provide automatic validity-checking functionality, and a range of methods implementing common operations on integer intervals and genomic ranges, from the calculation of distance between pairs of intervals to the identification of overlapping genomic ranges.
A short presentation of the basic classes defined in the GenomicRanges
package is available in one of the package vignettes, accessible as
vignette("GenomicRangesIntroduction"), while more detailed
information is provided in the other package vignettes, accessible as
browseVignettes("GenomicRanges").
The IRanges class
While the genomic space of many organisms is subdivided into multiple
sequences (e.g., chromosomes), many operations on genomic ranges take
place within individual sequences, where only integer positions matter.
The IRanges class provides a container for such “simple”
ranges that are defined by two out of three pieces of information:
- the start position of the range
- the width of the range
- the end position of the range
The IRanges() constructor function accepts those three
pieces of information in the arguments start=,
width=, and end=. For instance, we create two
integer ranges from their start position and width:
- one range starts at position 10 and has width 10
- one range starts at position 15 and has width 5
R
demo_iranges <- IRanges(start = c(10, 15), width = c(10, 5))
demo_iranges
OUTPUT
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 10 19 10
[2] 15 19 5We note how the object displays not only the start and width information that we requested for each range, but also the end position that is naturally computed from the other two pieces of information.
Challenge
Create the same two ranges as above, using the arguments
start= and end= of the IRanges()
constructor function.
R
IRanges(start = c(10, 15), end = c(19, 19))
OUTPUT
IRanges object with 2 ranges and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 10 19 10
[2] 15 19 5The start and end positions as well as the width of every interval
can be extracted as numeric vector using the functions
start(), end() and width(),
respectively.
R
start(demo_iranges)
OUTPUT
[1] 10 15R
end(demo_iranges)
OUTPUT
[1] 19 19R
width(demo_iranges)
OUTPUT
[1] 10 5Objects of the IRanges family extend the
Vector class, and are handled as unidimensional vectors in
terms of indexing. As such, individual ranges can be extracted by
integer index like any regular vector.
R
demo_iranges[1]
OUTPUT
IRanges object with 1 range and 0 metadata columns:
start end width
<integer> <integer> <integer>
[1] 10 19 10Metadata on IRanges
The IRanges class can accommodate metadata information
on each range, including names - passed to the names=
argument - and miscellaneous metadata passed as named vectors.
For instance, we create two ranges named “A” and “B”. Furthermore, we define metadata fields to store an example of character values and numeric values, respectively. Both the names and the values of the metadata fields are completely arbitrary in this example.
R
demo_with_metadata <- IRanges(
start = c(10, 15),
end = c(19, 19),
names = c("A", "B"),
character_metadata = c("control", "target"),
numeric_metadata = c(100, 200)
)
demo_with_metadata
OUTPUT
IRanges object with 2 ranges and 2 metadata columns:
start end width | character_metadata numeric_metadata
<integer> <integer> <integer> | <character> <numeric>
A 10 19 10 | control 100
B 15 19 5 | target 200The metadata columns can be extracted as a DataFrame
using the function mcols() (short for “metadata
columns”).
R
mcols(demo_with_metadata)
OUTPUT
DataFrame with 2 rows and 2 columns
character_metadata numeric_metadata
<character> <numeric>
A control 100
B target 200The character vector of names can be extracted using the function
names().
R
names(demo_with_metadata)
OUTPUT
[1] "A" "B"Similarly to named vector of base data types, individual ranges can be extracted by name.
R
demo_with_metadata["A"]
OUTPUT
IRanges object with 1 range and 2 metadata columns:
start end width | character_metadata numeric_metadata
<integer> <integer> <integer> | <character> <numeric>
A 10 19 10 | control 100Operations on IRanges
IRanges provide the basis for most operations on ranges
of numerical coordinates.
For instance, given two sets of ranges - a query set and a subject
set - the findOVerlaps() function can be used to find out
which pairs of ranges in the two sets overlap with each other.
R
query_iranges <- IRanges(
start = c(8, 16),
end = c(14, 18)
)
overlaps_iranges <- findOverlaps(query = query_iranges, subject = demo_iranges)
overlaps_iranges
OUTPUT
Hits object with 3 hits and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 1
[2] 2 1
[3] 2 2
-------
queryLength: 2 / subjectLength: 2The results are returned in the form of a Hits object,
which we have not introduced yet. A Hits object is
visualised as a table that comprises two integer columns named
queryHits and subjectHits. Each row in the
table reports an overlap between one range in the query set and one
range in the subject set, with the integer value in each column
indicating the index of the range in each set involved in the
overlap.
In this example, we confirm that the first range in the query set overlaps the first range in the subject set; while the second range in the query set overlaps both ranges in the subject set.
Going further
For downstream use, the two components can be extracted from
Hits objects using their names, respectively:
R
queryHits(overlaps_iranges)
OUTPUT
[1] 1 2 2R
subjectHits(overlaps_iranges)
OUTPUT
[1] 1 1 2While displayed as a table, Hits objects are actually
handled like vectors. Individual hits between one query range and one
subject range can be extracted their index:
R
overlaps_iranges[1]
OUTPUT
Hits object with 1 hit and 0 metadata columns:
queryHits subjectHits
<integer> <integer>
[1] 1 1
-------
queryLength: 2 / subjectLength: 2The GRanges class
Having defined integer ranges, the only additional information necessary to define genomic ranges is the name of the genomic sequence on which each range is located.
For instance, we define two genomic ranges, as follows:
- one genomic range on chromosome 1 (abbreviated “chr1”), from position 10 to 25
- one genomic range on chromosome 2 (abbreviated “chr2”), from position 20 to 35
To do so, we use the GRanges() constructor function. We
provide the sequence names as a character vector to the argument
seqnames=, and we provide both the start and end position
to the argument ranges= as an IRanges
object.
R
demo_granges <- GRanges(
seqnames = c("chr1", "chr2"),
ranges = IRanges(
start = c(10, 20),
end = c(25, 35))
)
demo_granges
OUTPUT
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 10-25 *
[2] chr2 20-35 *
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengthsIn the console, the object displays the sequence names in the
seqnames component, and the ranges in the form
start-end in the ranges component.
Furthermore, the example above also demonstrate that
GRanges objects possess a component called
strand; the symbol * indicates unstranded
genomic ranges, as we have not provided that information.
The strand information can be supplied to the strand=
argument, for instance:
R
demo_granges2 <- GRanges(
seqnames = c("chr1", "chr2"),
ranges = IRanges(
start = c(10, 20),
end = c(25, 35)),
strand = c("+", "-")
)
demo_granges2
OUTPUT
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 10-25 +
[2] chr2 20-35 -
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengthsFinally, the example above also demonstrate that GRanges
objects include a component called seqinfo, which can be
used to store information about each sequence that may be represented in
the seqnames component. In the latest example above, we
have not provide any information about any sequence. As such, the
seqinfo component was automatically populated with the
names of the sequences that we used to create the object, while the
remaining pieces of information were left unspecified, as
NA.
R
seqinfo(demo_granges2)
OUTPUT
Seqinfo object with 2 sequences from an unspecified genome; no seqlengths:
seqnames seqlengths isCircular genome
chr1 NA NA <NA>
chr2 NA NA <NA>The example above reveals that information about sequences include not only their respective name and length, but also whether they represent a circular polymer (e.g., plasmid), and the name of the genome that they are part of.
This information can be provided directly to the constructor when the
object is created, or edited on an existing object using the
seqinfo() accessor and the Seqinfo()
constructor:
R
seqinfo(demo_granges2) <- Seqinfo(
seqnames = c("chr1", "chr2"),
seqlengths = c(1234, 5678),
isCircular = c(FALSE, TRUE),
genome = c("homo_sapiens", "homo_sapiens")
)
demo_granges2
OUTPUT
GRanges object with 2 ranges and 0 metadata columns:
seqnames ranges strand
<Rle> <IRanges> <Rle>
[1] chr1 10-25 +
[2] chr2 20-35 -
-------
seqinfo: 2 sequences (1 circular) from homo_sapiens genomeThe start and end positions of the individual ranges as well as the
width of every interval can be extracted as numeric vector using the
functions start(), end() and
width(), respectively.
R
start(demo_granges2)
OUTPUT
[1] 10 20R
end(demo_granges2)
OUTPUT
[1] 25 35R
width(demo_granges2)
OUTPUT
[1] 16 16The sequence names and strand information can be extracted using the
functions seqnames() and strand(),
respectively.
R
seqnames(demo_granges2)
OUTPUT
factor-Rle of length 2 with 2 runs
Lengths: 1 1
Values : chr1 chr2
Levels(2): chr1 chr2R
strand(demo_granges2)
OUTPUT
factor-Rle of length 2 with 2 runs
Lengths: 1 1
Values : + -
Levels(3): + - *Metadata on GRanges
Similarly to IRanges, metadata can be passed directly to
the GRanges constructor function. For instance:
R
demo_granges3 <- GRanges(
seqnames = c("chr1", "chr2"),
ranges = IRanges(
start = c(10, 20),
end = c(25, 35)),
metadata1 = c("control", "target"),
metadata2 = c(1, 2)
)
demo_granges3
OUTPUT
GRanges object with 2 ranges and 2 metadata columns:
seqnames ranges strand | metadata1 metadata2
<Rle> <IRanges> <Rle> | <character> <numeric>
[1] chr1 10-25 * | control 1
[2] chr2 20-35 * | target 2
-------
seqinfo: 2 sequences from an unspecified genome; no seqlengthsImporting genomic ranges from files
Frequently, large collections of genomic ranges are imported from files rather than described in manually written code. In particular, genome-wide annotations of known gene features are distributed as files on websites such as the Ensembl FTP and the UCSC Genome Data sites.
Various file formats are commonly used to store genomic ranges in bioinformatics workflows. For instance, the BED (Browser Extensible Data) format is commonly found in Chromatin Immunoprecipitation Sequencing (ChIP-Seq), while GTF (Gene Transfer Format, GTF2.2) is the de facto standard file format to describe genomic features such as exons, transcripts, and genes.
In the following example, we import the gene model for Actin Beta (ACTB) from a small GTF file as a set of genomic ranges. The example file represents a subset of a GTF file for the Homo sapiens species, downloaded from the Ensembl FTP site. The original file contains more than 3 millions lines and 22 metadata fields, from which a subset was extracted into a smaller file for this lesson.
In particular, we use the import() generic defined in
the BiocIO
package - with methods implemented in the rtracklayer
package - as a versatile function that is capable of recognising common
file extensions and associating them with the appropriate method for
parsing each particular file format.
R
library(rtracklayer)
WARNING
Warning: replacing previous import 'S4Arrays::makeNindexFromArrayViewport' by
'DelayedArray::makeNindexFromArrayViewport' when loading 'SummarizedExperiment'R
actb_gtf_data <- rtracklayer::import("data/actb.gtf")
actb_gtf_data
OUTPUT
GRanges object with 267 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5526409-5563902 - | rtracklayer gene NA
[2] 7 5526409-5530601 - | rtracklayer transcript NA
[3] 7 5530542-5530601 - | rtracklayer exon NA
[4] 7 5529535-5529684 - | rtracklayer exon NA
[5] 7 5529535-5529657 - | rtracklayer CDS NA
... ... ... ... . ... ... ...
[263] 7 5540676-5540771 - | rtracklayer five_prime_utr NA
[264] 7 5529658-5529663 - | rtracklayer five_prime_utr NA
[265] 7 5561852-5562716 - | rtracklayer transcript NA
[266] 7 5562390-5562716 - | rtracklayer exon NA
[267] 7 5561852-5561949 - | rtracklayer exon NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB <NA>
[2] <NA> ENSG00000075624 ACTB ENST00000674681
[3] <NA> ENSG00000075624 ACTB ENST00000674681
[4] <NA> ENSG00000075624 ACTB ENST00000674681
[5] <NA> ENSG00000075624 ACTB ENST00000674681
... ... ... ... ...
[263] <NA> ENSG00000075624 ACTB ENST00000414620
[264] <NA> ENSG00000075624 ACTB ENST00000414620
[265] <NA> ENSG00000075624 ACTB ENST00000646584
[266] <NA> ENSG00000075624 ACTB ENST00000646584
[267] <NA> ENSG00000075624 ACTB ENST00000646584
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengthsGoing further
Individual methods for parsing specific file formats can be invoked
directly. For instance, in this case, the GTF file format being
identical to the GFF version 2 file format, we could have directly
invoked the function rtracklayer::import.gff2() with the
exact same effect.
Refer to the documentation of the rtracklayer package for the full list of methods available.
In the example above, the contents of the GTF file were imported into
a GRanges object. For each entry in the file, the sequence
name, start and end position, and strand information were used to
populate the dedicated components of the object, while all other pieces
of information are stored as separate columns of metadata.
From here on, this GRanges object can be manipulated
just like any of the other GRanges objects that we have
created earlier in this episode.
Operations on GRanges and the GRangesList class
As we have demonstrated so far, GRanges objects can be
manually defined or imported from files. Those often represent genomic
regions of interest, and databases of known genomic features,
respectively. Either way, a number of operations are commonly applied to
GRanges objects throughout bioinformatics workflows.
Subset
For instance, the subset() method is extremely
convenient to extract a set of genomic ranges matching a condition on
any component, including sequence name, start and end position, strand,
or any metadata field. In the example below, we extract all the records
of type transcript that start at position
5527147.
R
subset(actb_gtf_data, type == "transcript" & start == 5527147)
OUTPUT
GRanges object with 5 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5527147-5529949 - | rtracklayer transcript NA
[2] 7 5527147-5530581 - | rtracklayer transcript NA
[3] 7 5527147-5530604 - | rtracklayer transcript NA
[4] 7 5527147-5530604 - | rtracklayer transcript NA
[5] 7 5527147-5530604 - | rtracklayer transcript NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB ENST00000642480
[2] <NA> ENSG00000075624 ACTB ENST00000676397
[3] <NA> ENSG00000075624 ACTB ENST00000676319
[4] <NA> ENSG00000075624 ACTB ENST00000676189
[5] <NA> ENSG00000075624 ACTB ENST00000473257
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengthsSplit
Separately, the split() method is useful to divide a set
of genomic ranges initially stored in a single GRanges
object into groups that are stored in a named list of
GRanges objects. Conveniently, the GRangesList
class provides a container for efficiently displaying and processing
lists of GRanges objects.
In the example below, we first extract the subset of entries that
represent exons, before separating those exons by transcript identifier,
yielding the result as a GRangesList object.
R
actb_exons <- subset(actb_gtf_data, type == "exon")
actb_exons_by_transcript <- split(actb_exons, actb_exons$transcript_id)
actb_exons_by_transcript
OUTPUT
GRangesList object of length 23:
$ENST00000414620
GRanges object with 4 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5562574-5562790 - | rtracklayer exon NA
[2] 7 5540676-5540771 - | rtracklayer exon NA
[3] 7 5529535-5529663 - | rtracklayer exon NA
[4] 7 5529282-5529400 - | rtracklayer exon NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB ENST00000414620
[2] <NA> ENSG00000075624 ACTB ENST00000414620
[3] <NA> ENSG00000075624 ACTB ENST00000414620
[4] <NA> ENSG00000075624 ACTB ENST00000414620
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$ENST00000417101
GRanges object with 3 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5529806-5529982 - | rtracklayer exon NA
[2] 7 5529535-5529663 - | rtracklayer exon NA
[3] 7 5529235-5529400 - | rtracklayer exon NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB ENST00000417101
[2] <NA> ENSG00000075624 ACTB ENST00000417101
[3] <NA> ENSG00000075624 ACTB ENST00000417101
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
$ENST00000425660
GRanges object with 7 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5530524-5530601 - | rtracklayer exon NA
[2] 7 5529535-5529663 - | rtracklayer exon NA
[3] 7 5529161-5529400 - | rtracklayer exon NA
[4] 7 5529019-5529059 - | rtracklayer exon NA
[5] 7 5528281-5528719 - | rtracklayer exon NA
[6] 7 5528004-5528185 - | rtracklayer exon NA
[7] 7 5527156-5527891 - | rtracklayer exon NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB ENST00000425660
[2] <NA> ENSG00000075624 ACTB ENST00000425660
[3] <NA> ENSG00000075624 ACTB ENST00000425660
[4] <NA> ENSG00000075624 ACTB ENST00000425660
[5] <NA> ENSG00000075624 ACTB ENST00000425660
[6] <NA> ENSG00000075624 ACTB ENST00000425660
[7] <NA> ENSG00000075624 ACTB ENST00000425660
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengths
...
<20 more elements>When printing the object above in the console, the first line
confirms the class of the object as GRrangesList, while
each named GRanges in that list is introduced by the dollar
sign and the name of that item, just like regular named lists in base
R.
Length
By nature, many of the methods applicable to list
objects can be directly applied to GRangesList objects. For
instance, the lengths() function can be used on
GRangesList to display the length of each
GRanges object in the list as an integer vector.
In the latest example above, we can compute the number of exons in
each transcript as the length of each GRanges object within
the GRangesList:
R
lengths(actb_exons_by_transcript)
OUTPUT
ENST00000414620 ENST00000417101 ENST00000425660 ENST00000432588 ENST00000443528
4 3 7 5 3
ENST00000462494 ENST00000464611 ENST00000473257 ENST00000477812 ENST00000480301
5 3 5 5 2
ENST00000484841 ENST00000493945 ENST00000642480 ENST00000645025 ENST00000645576
5 6 5 4 5
ENST00000646584 ENST00000646664 ENST00000647275 ENST00000674681 ENST00000675515
2 6 3 6 6
ENST00000676189 ENST00000676319 ENST00000676397
6 3 6 Challenge
Importantly, the function lengths() (with a final
s) demonstrated above is different from the function
length() (without s). The former is meant to
be used on list objects, returning a vector giving the length of each
element in the list; while the latter returns a single numeric scalar
giving the length of the list itself (i.e., the number of elements in
the list).
What does length(actb_exons_by_transcript) return, and
what does this number represent biologically?
R
length(actb_exons_by_transcript)
OUTPUT
[1] 23This code returns the single integer value 23, which is
the number of GRanges in the GRangesList
object and the number of transcripts for the gene ACTB.
Subset by overlap
Possibly one of the most common operations when working with genomic ranges is to subset arbitrarily large collections of genomic ranges to those located in a specific region of the genome; for instance, when visualising information as tracks in a genome browser.
To demonstrate, we manually define a new GRanges
representing a region of interest that we will use to extract all of the
genomic ranges imported earlier from the GTF file which overlap that
region of interest.
R
region_of_interest <- GRanges(
seqnames = "7",
ranges = IRanges(start = 5525830, end = 5531239)
)
actb_in_region <- subsetByOverlaps(x = actb_gtf_data, ranges = region_of_interest)
actb_in_region
OUTPUT
GRanges object with 256 ranges and 7 metadata columns:
seqnames ranges strand | source type score
<Rle> <IRanges> <Rle> | <factor> <factor> <numeric>
[1] 7 5526409-5563902 - | rtracklayer gene NA
[2] 7 5526409-5530601 - | rtracklayer transcript NA
[3] 7 5530542-5530601 - | rtracklayer exon NA
[4] 7 5529535-5529684 - | rtracklayer exon NA
[5] 7 5529535-5529657 - | rtracklayer CDS NA
... ... ... ... . ... ... ...
[252] 7 5529535-5529657 - | rtracklayer CDS NA
[253] 7 5529655-5529657 - | rtracklayer start_codon NA
[254] 7 5529282-5529400 - | rtracklayer exon NA
[255] 7 5529282-5529400 - | rtracklayer CDS NA
[256] 7 5529658-5529663 - | rtracklayer five_prime_utr NA
phase gene_id gene_name transcript_id
<integer> <character> <character> <character>
[1] <NA> ENSG00000075624 ACTB <NA>
[2] <NA> ENSG00000075624 ACTB ENST00000674681
[3] <NA> ENSG00000075624 ACTB ENST00000674681
[4] <NA> ENSG00000075624 ACTB ENST00000674681
[5] <NA> ENSG00000075624 ACTB ENST00000674681
... ... ... ... ...
[252] <NA> ENSG00000075624 ACTB ENST00000414620
[253] <NA> ENSG00000075624 ACTB ENST00000414620
[254] <NA> ENSG00000075624 ACTB ENST00000414620
[255] <NA> ENSG00000075624 ACTB ENST00000414620
[256] <NA> ENSG00000075624 ACTB ENST00000414620
-------
seqinfo: 1 sequence from an unspecified genome; no seqlengthsLike the subset() method, the
subsetByOverlaps() method returns a new
GRanges object. We can visually compare the information
printed in the object (256 ranges in the new subsetted object, relative
to 267 ranges in the original object), or we can programmatically
compare the length of the two objects to check whether the new
GRanges object is any smaller than the original
GRanges object:
R
length(actb_in_region) - length(actb_gtf_data)
OUTPUT
[1] -11In the example above, we learn that the new GRanges
object has 11 records less than the original GRanges
object.
Going further
Many more methods exist to operate on GRanges and
GRangesList objects than what could be demonstrated
here.
You can find the full list of functions defined in the
GenomicRanges package on the index page of the package
documentation, accessible using
help(package="GenomicRanges"). You can also find more
examples and use cases in the package vignettes, accessible using
browseVignettes("GenomicRanges").
Key Points
- The
GenomicRangespackage defines classes to represent ranges of coordinates on a genomic scale. - The
GenomicRangespackage also defines methods to efficiently process genomic ranges. - The
rtracklayerpackage provides functions to import and export genomic ranges from and to common genomic file formats.