This package calculates Fst from SNP inputs. SNPs impletmented the Fst function from the package KIRS, with more efficient coding.
A measure of population differentiation due to genetic structure. In this function, Fst is estimated from one of genetic polymorphism data, single-nucleotide polymorphisms(SNP). Calculation implemented by Hudson method in Hudson(1992).
The main function in the package is Fst.
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sim_SNP: SNP datasets could be simulated with this function. (But they are rather unrealistic, so do not use them forany purpose other than package tutorial.) -
data.prep: Preapre data for Fst calculation. Parse SNP dataset by population before calculating Fst to save time. -
FST: A measure of population differentiation due to genetic structure. In this function, Fst is estimated from one of genetic polymorphism data, single-nucleotide polymorphisms(SNP). Calculation implemented by Hudson method in Hudson(1992).
#install.packages("devtools")
library(devtools)
devtools::install_github("https://github.com/FayeFang17/625/")
library(bios625)
To view the tutorial(vignette) associated with this package, check vignetttes/tutorial.rmd
SNP_example=sim_SNP(method="SNP")
label=sim_SNP(method="label")
SNP=data.prep(SNP_example,label)
FST(SNP$'1',SNP$'2')
This package was created in 2021 by Faye Fang.
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Kridsadakorn Chaichoompu, Fentaw Abegaz, Sissades Tongsima, Philip James Shaw, Anavaj Sakuntabhai, Luisa Pereira, and Kristel Van Steen (2018). KRIS: Keen and Reliable Interface Subroutines for Bioinformatic Analysis. R package version 1.1.6. URL: https://CRAN.R-project.org/package=KRIS
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Bhatia, G., Patterson, N., Sankararaman, S., and Price, A.L. (2013).
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Hudson, R.R., Slatkin, M., and Maddison, W.P. (1992). Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583-589.