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zalpha: an R package for the identification of regions of the genome under selection

zalpha: an R package for the identification of regions of the genome under selection
zalpha: an R package for the identification of regions of the genome under selection
Detecting evidence of selection and evolution in population genomes is crucial to understanding the history and the selective pressures experienced by a population. While there are many statistics for identifying regions of the genome under selection, there is a need for software to enable reproducible, standardised results. The statistics implemented in the zalpha R package use the relationships and correlations in genetic variation to find patterns that could be indicative of a selective sweep.

The methods contained within this R package are a development of the statistics published by Jacobs et al. (2016). This package allows users to run a range of selection statistics on genetic data, which previously were not made publicly available in software. The software is designed to be flexible to allow users to efficiently combine statistics and is open source.

The package also allows users to utilise a linkage disequilibrium (LD) profile, taking into ac-count expected relationships between alleles, ultimately increasing the power of the statistics. This is important as LD varies immensely along the genome, with recombination the biggest contributor to LD fluctuations (Jeffreys et al., 2001)
Horscroft, Clare
6ed6a58f-5fe9-4be0-a92e-bee5ea43aa8c
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Sluckin, T.J.
8dbb6b08-7034-4ae2-aa65-6b80072202f6
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64
Horscroft, Clare
6ed6a58f-5fe9-4be0-a92e-bee5ea43aa8c
Pengelly, Reuben
af97c0c1-b568-415c-9f59-1823b65be76d
Sluckin, T.J.
8dbb6b08-7034-4ae2-aa65-6b80072202f6
Collins, Andrew
7daa83eb-0b21-43b2-af1a-e38fb36e2a64

Horscroft, Clare, Pengelly, Reuben, Sluckin, T.J. and Collins, Andrew (2020) zalpha: an R package for the identification of regions of the genome under selection. The Journal of Open Source Software, 5 (56), [2638]. (doi:10.21105/joss.02638).

Record type: Article

Abstract

Detecting evidence of selection and evolution in population genomes is crucial to understanding the history and the selective pressures experienced by a population. While there are many statistics for identifying regions of the genome under selection, there is a need for software to enable reproducible, standardised results. The statistics implemented in the zalpha R package use the relationships and correlations in genetic variation to find patterns that could be indicative of a selective sweep.

The methods contained within this R package are a development of the statistics published by Jacobs et al. (2016). This package allows users to run a range of selection statistics on genetic data, which previously were not made publicly available in software. The software is designed to be flexible to allow users to efficiently combine statistics and is open source.

The package also allows users to utilise a linkage disequilibrium (LD) profile, taking into ac-count expected relationships between alleles, ultimately increasing the power of the statistics. This is important as LD varies immensely along the genome, with recombination the biggest contributor to LD fluctuations (Jeffreys et al., 2001)

Text
10.21105.joss.02638 - Version of Record
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More information

Submitted date: 8 August 2020
Accepted/In Press date: 3 December 2020
Published date: 5 December 2020

Identifiers

Local EPrints ID: 445659
URI: http://eprints.soton.ac.uk/id/eprint/445659
PURE UUID: 1b694222-df81-4f23-b4dc-45e76722661e
ORCID for Reuben Pengelly: ORCID iD orcid.org/0000-0001-7022-645X
ORCID for T.J. Sluckin: ORCID iD orcid.org/0000-0002-9163-0061
ORCID for Andrew Collins: ORCID iD orcid.org/0000-0001-7108-0771

Catalogue record

Date deposited: 05 Jan 2021 17:32
Last modified: 18 Feb 2021 17:22

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Contributors

Author: Clare Horscroft
Author: Reuben Pengelly ORCID iD
Author: T.J. Sluckin ORCID iD
Author: Andrew Collins ORCID iD

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