Package 'polyRADtutorials'

Title: Supplementary Tutorials for polyRAD
Description: Additional tutorials for polyRAD that are not included in its package vignettes due to file size, computational time, and/or package dependencies.
Authors: Lindsay V. Clark [aut, cre] , U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <[email protected]>
License: GPL (>= 2)
Version: 0.1
Built: 2024-11-01 11:33:43 UTC
Source: https://github.com/lvclark/polyRADtutorials

Help Index

Read depth data for tetraploid Miscanthus sacchariflorus on chromosome 3

Description

Allelic read depth data from a RAD-seq experiment across 270 tetraploid Miscanthus sacchariflorus and 3414 loci on chromsome 3.

Usage

data("Msa_4x_chr3")

Format

A RADdata object generated by VCF2RADdata, prior to genotype calling.

Source

Lindsay V. Clark, Xiaoli Jin, Karen K. Petersen, Kossanou G. Anzoua, Larissa Bagmet, Pavel Chebukin, Martin Deuter, Elena Dzyubenko, Nicolay Dzyubenko, Kweon Heo, Douglas A. Johnson, Uffe Jorgensen, Jens B. Kjeldsen, Hironori Nagano, Junhua Peng, Andrey Sabitov, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Stephen P. Long, and Erik J. Sacks (2019) "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centered around the Yellow Sea." Annals of Botany 124(4): 731-748. doi:10.1093/aob/mcy161.

Data available in VCF format on the Illinois Data Bank: doi:10.13012/B2IDB-8170405_V1

References

Marker positions are with respect to the M. sinensis v7 reference genome: https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Msinensis_er

Therese Mitros, Adam M. Session, Brandon T. James, Guohong Albert Wu, Mohammad B. Belaffif, Lindsay V. Clark, Shengqiang Shu, Hongxu Dong, Adam Barling, Jessica R. Holmes, Jessica E. Mattick, Jessen V. Bredeson, Siyao Liu, Kerrie Farrar, Katarzyna Glowacka, Stanislaw Jezowski, Kerrie Barry, Won Byoung Chae, John A. Juvik, Justin Gifford, Adebosola Oladeinde, Toshihiko Yamada, Jane Grimwood, Nicholas H. Putnam, Jose De Vega, Susanne Barth, Manfred Klaas, Trevor Hodkinson, Laigeng Li, Xiaoli Jin, Junhua Peng, Chang Yeon Yu, Kweon Heo, Ji Hye Yoo, Bimal Kumar Ghimire, Iain S. Donnison, Jeremy Schmutz, Matthew E. Hudson, Erik J. Sacks, Stephen P. Moose, Kankshita Swaminathan, and Daniel S. Rokhsar (2020) "Genome biology of the paleotetraploid perennial biomass crop Miscanthus."" Nature Communications 11:5442. doi:10.1038/s41467-020-18923-6

Examples

data(Msa_4x_chr3)
Msa_4x_chr3

Collection locations for Miscanthus sacchariflorus

Description

Latitude and longitude data for accessions within the Msa_4x_chr3 dataset.

Usage

data("Msa_latlong")

Format

A data frame with 270 observations on the following 3 variables.

Accession

Accession names, matching the genetic dataset.

Latitude

Latitude of collection.

Longitude

Longitude of collection.

Source

Lindsay V. Clark, Xiaoli Jin, Karen K. Petersen, Kossanou G. Anzoua, Larissa Bagmet, Pavel Chebukin, Martin Deuter, Elena Dzyubenko, Nicolay Dzyubenko, Kweon Heo, Douglas A. Johnson, Uffe Jorgensen, Jens B. Kjeldsen, Hironori Nagano, Junhua Peng, Andrey Sabitov, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Stephen P. Long, and Erik J. Sacks (2019) "Population structure of Miscanthus sacchariflorus reveals two major polyploidization events, tetraploid-mediated unidirectional introgression from diploid M. sinensis, and diversity centered around the Yellow Sea." Annals of Botany 124(4): 731-748. doi:10.1093/aob/mcy161.

Data available at the Illinois Data Bank: doi:10.13012/B2IDB-0170190_V3

Examples

data(Msa_latlong)
head(Msa_latlong)