[](https://f1000research.com/articles/10-141)
[](https://doi.org/10.1101/gr.265934.120)
[](https://www.bioconductor.org/packages/periodicDNA)
[](https://www.tidyverse.org/lifecycle/#production)
[](https://github.com/js2264/periodicDNA)
[](https://www.gnu.org/licenses/gpl-3.0.en.html)
[](https://codecov.io/gh/js2264/periodicDNA?branch=master)
[](https://github.com/js2264/periodicDNA/actions)
# periodicDNA <img src="man/figures/logo.png" align="right" alt="" />
## Introduction
This R package helps the user identify k-mers (e.g. di- or
tri-nucleotides) present periodically in a set of genomic loci (typically
regulatory elements). It is not aimed at identifying motifs separated by a
conserved distance; for this type of analysis, please visit
[MEME](http://meme-suite.org) website.
## Installation
periodicDNA is available in Bioconductor. To install the current release use:
```r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("periodicDNA")
```
For advanced users, the most recent periodicDNA can be installed
from Github as follows (might be buggy):
```r
install.packages("devtools")
devtools::install_github("js2264/periodicDNA")
library(periodicDNA)
```
## Citation
If you are using periodicDNA in your research, please cite:
> [periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA](https://f1000research.com/articles/10-141)
> **J. Serizay** & J. Ahringer
> F1000Research, 2021
> [Distinctive regulatory architectures of germline-active and somatic genes in C. elegans](https://genome.cshlp.org/content/early/2020/10/21/gr.265934.120.abstract)
> **J. Serizay**, Y. Dong, J. Jänes, M. Chesney, C. Cerrato & J. Ahringer
> Genome Research, 2020
## How to use periodicDNA
periodicDNA includes a vignette where its usage is
illustrated. To access the vignette, please use:
```r
vignette('periodicDNA')
```
## Main functions
The two main user-level functions of periodicDNA are `getPeriodicity()` and
`getPeriodicityTrack()`.
* `getPeriodicity()` is used to compute the power spectral density
(PSD) of a chosen k-mer (i.e. `TT`) in a set of sequences. The PSD
score at a given period indicates the strength of the k-mer at
this period.
* `getPeriodicityTrack()` can be used to generate linear tracks representing
the periodicity strength of a given k-mer at a chosen period, over genomic
loci of interest.
### `getPeriodicity()` function
```r
data(ce11_TSSs)
PSDs <- getPeriodicity(
ce11_TSSs[['Ubiq.']],
genome = 'BSgenome.Celegans.UCSC.ce11',
motif = 'TT',
BPPARAM = MulticoreParam(12),
n_shuffling = 100
)
plotPeriodicityResults(PSDs)
```
### `getPeriodicityTrack()` function
```r
data(ce11_proms)
WW_10bp <- getPeriodicityTrack(
genome = 'BSgenome.Celegans.UCSC.ce11',
granges = ce11_proms,
motif = 'WW',
period = 10,
bw_file = 'WW-10-bp-periodicity_over-proms.bw',
BPPARAM = MulticoreParam(12)
)
```
**Warning**: It is recommended to run this command across many processors
using BiocParallel. This command typically takes one day to produce
a periodicity track over 15,000 GRanges of 150 bp (with default parameters)
using `BPPARAM = MulticoreParam(12)`.
It is highly recommended to run this command in a new `screen` session.
## Contributions
Code contributions, bug reports, fixes and feature requests are most welcome.
Please make any pull requests against the master branch at
https://github.com/js2264/periodicityDNA
and file issues at https://github.com/js2264/periodicityDNA/issues
## License
**periodicDNA** is licensed under the GPL-3 license.
