This package is posted on CRAN.
Updog provides a suite of methods for genotyping polyploids from next-generation sequencing (NGS) data. It does this while accounting for many common features of NGS data: allele bias, overdispersion, and sequencing error. It is named updog for “Using Parental Data for Offspring Genotyping” because we originally developed the method for full-sib populations, but it works now for more general populations. The method is described in detail Gerard et. al. (2018) <doi:10.1534/genetics.118.301468>. Additional details concerning prior specification are described in Gerard and Ferrão (2020) <doi:10.1093/bioinformatics/btz852>.
The main functions are flexdog()
and multidog()
, which provide many
options for the distribution of the genotypes in your sample. A novel
genotype distribution is included in the class of proportional normal
distributions (model = "norm"
). This is the default prior distribution
because it is the most robust to varying genotype distributions, but
feel free to use more specialized priors if you have more information on
the data.
Also provided are:
filter_snp()
: filter out SNPs based on the output of multidog()
.
format_multidog()
: format the output of multidog()
in terms of a
multidimensional array.
Plot methods. Both flexdog()
and multidog()
have plot methods.
See the help files of plot.flexdog()
and plot.multidog()
for
details.
Functions to simulate genotypes (rgeno()
) and read-counts
(rflexdog()
). These support all of the models available in
flexdog()
.
Functions to evaluate oracle genotyping performance:
oracle_joint()
, oracle_mis()
, oracle_mis_vec()
, and
oracle_cor()
. We mean “oracle” in the sense that we assume that
the entire data generation process is known (i.e. the genotype
distribution, sequencing error rate, allele bias, and overdispersion
are all known). These are good approximations when there are a lot
of individuals (but not necessarily large read-depth).
You can install updog from CRAN in the usual way:
install.packages("updog")
You can install the current (unstable) version of updog from GitHub with:
# install.packages("devtools")
devtools::install_github("dcgerard/updog")
Please cite
Gerard, D., Ferrão, L. F. V., Garcia, A. A. F., & Stephens, M. (2018). “Genotyping Polyploids from Messy Sequencing Data”. Genetics, 210(3), 789-807. doi: 10.1534/genetics.118.301468.
Or, using BibTex:
@article {gerard2018genotyping,
author = {Gerard, David and Ferr{\~a}o, Lu{\'i}s Felipe Ventorim and Garcia, Antonio Augusto Franco and Stephens, Matthew},
title = {Genotyping Polyploids from Messy Sequencing Data},
volume = {210},
number = {3},
pages = {789--807},
year = {2018},
doi = {10.1534/genetics.118.301468},
publisher = {Genetics},
issn = {0016-6731},
URL = {https://doi.org/10.1534/genetics.118.301468},
journal = {Genetics}
}
If you are using the proportional normal prior class (model = "norm"
),
which is also the default prior, then please also cite:
Gerard D, Ferrão L (2020). “Priors for Genotyping Polyploids.” Bioinformatics, 36(6), 1795-1800. ISSN 1367-4803, doi: 10.1093/bioinformatics/btz852.
Or, using BibTex:
@article{gerard2020priors,
title = {Priors for Genotyping Polyploids},
year = {2020},
journal = {Bioinformatics},
publisher = {Oxford University Press},
volume = {36},
number = {6},
pages = {1795--1800},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btz852},
author = {David Gerard and Lu{\'i}s Felipe Ventorim Ferr{\~a}o},
}