<!-- README.md is generated from README.Rmd. Please edit that file -->
# GenomicTuples
<!-- badges: start -->
[](https://bioconductor.org/checkResults/release/bioc-LATEST/GenomicTuples)
[](https://github.com/PeteHaitch/GenomicTuples/actions)
[](https://codecov.io/gh/PeteHaitch/GenomicTuples?branch=master)
<!-- badges: end -->
**GenomicTuples** is an R/Bioconductor package that defines general
purpose containers for storing and manipulating *genomic tuples*. A
genomic tuple of size `m` is of the form
`chromosome:strand:{pos_1, pos_2, ..., pos_m}` where `pos_1` <
`pos_2` < `...` < `pos_m` are positions along the chromosome.
**GenomicTuples** aims to provide functionality for tuples of genomic
co-ordinates that are analogous to those available for genomic ranges in
the
***[GenomicRanges](https://bioconductor.org/packages/3.14/GenomicRanges)***
R/Bioconductor package.
## Installation
Most users will want to install GenomicTuples using the current release
of Bioconductor using:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("GenomicTuples")
```
The master branch of this repository is the development version of the
package. The development version of **GenomicTuples** can only be
installed using the development version of Bioconductor. Please first
read [these instructions on installing the development version of
Bioconductor](http://www.bioconductor.org/developers/how-to/useDevel/);
**GenomicTuples** can then be installed by:
``` r
if (!requireNamespace("BiocManager", quietly = TRUE)) {
install.packages("BiocManager")
}
BiocManager::install("GenomicTuples", version = "devel")
```
## Example
Here we use the **GenomicTuples** package to define two *GTuples*
objects, one containing 5 3-tuples and one containing 3 3-tuples,
demonstrate how to identify ‘equal’ genomic tuples, and how this
calculation would be incorrect if we were to mistakenly treat these
genomic tuples as genomic ranges:
``` r
# Load the package
library(GenomicTuples)
# Create a GTuples object containing 5 3-tuples
x <- GTuples(
seqnames = c('chr1', 'chr1', 'chr1', 'chr1', 'chr2'),
tuples = matrix(
c(10L, 20L, 30L,
10L, 20L, 30L,
10L, 20L, 35L,
10L, 25L, 30L,
10L, 20L, 30L),
ncol = 3,
byrow = TRUE),
strand = c('+', '-', '*', '+', '+'))
x
#> GTuples object with 5 x 3-tuples and 0 metadata columns:
#> seqnames pos1 pos2 pos3 strand
#> [1] chr1 10 20 30 +
#> [2] chr1 10 20 30 -
#> [3] chr1 10 20 35 *
#> [4] chr1 10 25 30 +
#> [5] chr2 10 20 30 +
#> ---
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
# Create a new GTuples object containing 3 3-tuples by subsetting x
y <- x[2:4]
y
#> GTuples object with 3 x 3-tuples and 0 metadata columns:
#> seqnames pos1 pos2 pos3 strand
#> [1] chr1 10 20 30 -
#> [2] chr1 10 20 35 *
#> [3] chr1 10 25 30 +
#> ---
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
# Find equal genomic tuples
subsetByOverlaps(x, y, type = "equal")
#> GTuples object with 3 x 3-tuples and 0 metadata columns:
#> seqnames pos1 pos2 pos3 strand
#> [1] chr1 10 20 30 -
#> [2] chr1 10 20 35 *
#> [3] chr1 10 25 30 +
#> ---
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
# Find equal genomic tuples when ignoring strand
subsetByOverlaps(x, y, type = "equal", ignore.strand = TRUE)
#> GTuples object with 4 x 3-tuples and 0 metadata columns:
#> seqnames pos1 pos2 pos3 strand
#> [1] chr1 10 20 30 +
#> [2] chr1 10 20 30 -
#> [3] chr1 10 20 35 *
#> [4] chr1 10 25 30 +
#> ---
#> seqinfo: 2 sequences from an unspecified genome; no seqlengths
# Note that if were to mistakenly treat these as genomic ranges, then the set
# of 'equal' genomic tuples would be incorrect since treating these tuples as
# ranges ignores the "internal positions" (pos2).
# The set of overlaps when correctly treated as genomic tuples:
findOverlaps(x, y, type = "equal")
#> Hits object with 3 hits and 0 metadata columns:
#> queryHits subjectHits
#> <integer> <integer>
#> [1] 2 1
#> [2] 3 2
#> [3] 4 3
#> -------
#> queryLength: 5 / subjectLength: 3
# The set of overlaps when incorrected treated as genomic ranges:
findOverlaps(as(x, "GRanges"), as(y, "GRanges"), type = 'equal')
#> Hits object with 4 hits and 0 metadata columns:
#> queryHits subjectHits
#> <integer> <integer>
#> [1] 1 3
#> [2] 2 1
#> [3] 3 2
#> [4] 4 3
#> -------
#> queryLength: 5 / subjectLength: 3
```
**GenomicTuples** includes extensive documentation available through the
R help system:
``` r
# See all documentation for the package
help(package = "GenomicTuples")
# See documentation for the GTuples class
?GTuples
```
The package also includes a comprehensive vignette that explains in
greater detail the different between a genomic tuple and a genomic
range, when genomic tuples may be usefu, and common operations on
genomic tuples. The vignette can be viewed at
<http://bioconductor.org/packages/release/bioc/vignettes/GenomicTuples/inst/doc/GenomicTuplesIntroduction.html>
or accessed from R using:
``` r
vignette("GenomicTuplesIntroduction", package = "GenomicTuples")
```
## Citation
**GenomicTuples** has been published in The Journal of Open Source
Software, <http://joss.theoj.org/papers/10.21105/joss.00020>.
If you use **GenomicTuples**, please cite the paper and software
version. This can be done as follows:
``` r
citation("GenomicTuples")
#>
#> To cite GenomicTuples in publications, please use:
#>
#> Peter F Hickey, (2016) Representation and Manipulation of Genomic
#> Tuples in R. JOSS: doi:10.21105/joss.00020
#>
#> A BibTeX entry for LaTeX users is
#>
#> @Article{,
#> title = {Representation and Manipulation of Genomic Tuples in R},
#> author = {Peter F Hickey},
#> year = {2016},
#> journal = {The Journal of Open Source Software},
#> doi = {http://dx.doi.org/10.21105/joss.00020},
#> url = {http://joss.theoj.org/papers/64b99f363d24b8a7e9025188183e9865},
#> }
packageVersion("GenomicTuples")
#> [1] '1.27.0'
```
## License
**GenomicTuples** is licensed under [Artistic
2.0](https://www.r-project.org/Licenses/Artistic-2.0).
## Code of Conduct
Please note that the **GenomicTuples** project is released with a
[Contributor Code of
Conduct](http://bioconductor.org/about/code-of-conduct/). By
contributing to this project, you agree to abide by its terms.
