README.md

In liqingsongplus/Genetic-diversity: genetic deversity

genetic

You can compute genetic diversity about SNPs in HMP format.

Installation

You can install the released version of genetic from the development version from GitHub with:

# install.packages("devtools")
devtools::install_github("liqingsongplus/Genetic-diversity")

Example

This is a basic example which shows you how to solve a common problem:

You can use GenoToHmp() get the HMP format file of SNPs from genotype file that conducted by novoSNP, such as:

library(genetic)
data(E5b_geno) # the output file from 
GenoToHmp(E5b_geno, "E5b")

else:

data(E5b_hmp)      # load the SNPs data of common carp E5b CDS   
diveristy(E5b_hmp) # compute the genetic diversity of SNPs
ld_plot(E5b_hmp,E5b_hmp$pos) # LDheatmap.pdf will be generated in the current directory

liqingsongplus/Genetic-diversity documentation built on Dec. 21, 2021, 10:51 a.m.