diff --git a/paper/paper.bib b/paper/paper.bib index edfd48642ca063ca7cf99c3c44883eb5c6cab38d..9c400de508dbe0f916b8065b0a671a59caf7c012 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -4,6 +4,15 @@ Title = {{A Primer of Molecular Population Genetics}}, Year = 2019 } +@Article{Gautier:2017, + author = {{Gautier}, M., and {Klassmann}, A. and {Vitalis}, R.}, + title = {rehh2.0: a reimplementation of the R package rehh to detect positive selection from haplotype structure}, + journal = {Molecular Ecology Resources}, + year = {2017}, + volume = {17}, + number = {1}, + pages = {78-90}, +} @article{Jacobs:2016, title="{Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps}", author={{Jacobs}, G.S., and {Sluckin}, T.J. and {Kivisild}, T.}, @@ -42,6 +51,15 @@ pages={23--35}, year={1974}, } +@Article{Pfeifer:2014, + title = {PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R}, + journal = {Molecular Biology and Evolution}, + year = {2014}, + author = {{Pfeifer}, B., and {Wittelsbuerger}, U. and {Ramos-Onsins}, S.E. and {Lercher}, M.J.}, + volume = {31}, + pages = {1929-1936}, + doi = {10.1093/molbev/msu136}, +} @incollection{Vitti:2013, author = {{Vitti}, J.J., and {Grossman}, S.R. and {Sabeti}, P.C.}, title = {Detecting Natural Selection in Genomic Data}, diff --git a/paper/paper.md b/paper/paper.md index c27582456e1886633ce20c7de7cc697d311ed61f..54979d487b37807fbcdd22b6cc52d5b13fa1a5dd 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -92,6 +92,8 @@ There are many statistics included in the package for adjusting for expected $r^ The output of the functions is in list format. The SNP positions and the values of the statistic(s) are stored in vectors of equal length in the list. Users can then identify outlying SNPs in their data that are candidate regions for selection. +There are a few other R packages that can be used for selection scans, although none utilise the $Z_{\alpha}$ statistics described here. These include `PopGenome` [@Pfeifer:2014], which calcualtes Kelly's $Z_{nS}$ among other methods, and `rehh` [@Gautier:2017], which implements extended haplotype homozygosity (EHH) and related statistics. + # Conclusion This new package allows researchers to calculate the $Z_{\alpha}$ suite of selection statistics efficiently using the free, open source R platform. These statistics had previously not been publicly available in software. The package's flexibility allows the user to adjust the statistics for the expected $r^2$ value via an LD profile in a variety of ways, and enables the adjustment of the base statistics to create new and novel methods. diff --git a/paper/paper.pdf b/paper/paper.pdf new file mode 100644 index 0000000000000000000000000000000000000000..f99ae307e9eb67927bcee55ed1c4f0b8c54033e1 Binary files /dev/null and b/paper/paper.pdf differ