htspop
is a R package designed for analysis and computation of population
genetic statistics using high-dimensional biallelic data. It includes the
following statistics:
You may install the development version, using devtools
# devtools instalation
devtools::install_github("andremrsantos/htspop")
## Simulate genotype matrix
geno <- matrix(sample(0:2, 100, replace = TRUE), ncol = 10)
## Convert into Allele Count structure
ac <- ac_matrix_from_genotype(geno)
## Run F Statistics
jackknife(f4_stat(ac, c(1, 2, 3, 4)))
jackknife(f3_stat(ac, c(1, 2, 3)))
## Run D Statistics
jackknife(d_stat(ac, c(1, 2, 3, 4)))
## Compute Weir & Cockerham Fst and Nei Standard Genetic Distance
fst(ac, "wc")
nei(ac)
If you use htspop
, please specify the version and cite:
Ribeiro-dos-Santos, AM, de Souza, SJ (2018) Htspop: high-troughput sequencing population genetic functions.
Create an issue to report bugs, propose new functions or ask for help. Please take in consideration this project is under development.
André M. Ribeiro-dos-Santos, andremrsantos@gmail.com
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