IAS-Breeding
智能农业育种解决方案
IAS Breeding 是一款专门用于方差成分和育种值分析的软件。它包括线性混合模型、机器学习非线性模型和贝叶斯模型。该软件提供两种分析平台：离线软件分析（R语言嵌入C++）和在线网页分析。
IAS-breeding特点:
版本丰富
Linux C++, R, 在线网页
运算高效
Fast C++ math library
用户友好
交互网页和R版本
功能丰富
遗传力估计, 育种值估计
IAS-breeding 功能:
方差组分计算
AI-REML
遗传参数估计
遗传力和遗传相关
基于系谱亲缘关系矩阵 BLUP方法
线性混合模型
基因组预测
基因组亲缘关系矩阵，线性混合模型
开发者：蔡文涛
联系方式：caiwentao@caas.cn
表型基本统计
表型分布统计
方差组分计算
遗传力
IASbreeding V0.1.0 can calculate kinship matrix, variance component analysis using linear mixed model, breeding value using BLUP. The core algorithm of IASbreeding is built using Rcpp and RcppEigen.
Start an R session using RStudio and run these lines:
install.packages("IASbreeding_0.1.0.zip", repos = NULL)
install.packages("Rcpp","RcppEigen")
library(IASbreeding)
library(Rcpp)
library(RcppEigen)
phe_file <- system.file("extdata", "Phenotype.txt", package = "IASbreeding", mustWork = TRUE)
pheno <- read.table(phe_file,header=TRUE)
ped_file <- system.file("extdata", "Pedigree.txt", package = "IASbreeding", mustWork = TRUE)
ped <- read.table(ped_file,header=TRUE)
newped<-pedcheck(ped)
A<-Akin(newped)
Results <- IASBLUP(BW56 ~ 1 + Sex + Condition,random = "ID", kinship = A, max_iter = 20, data = pheno)
bed_file <- system.file("extdata", "Genotype.bed", package = "IASbreeding", mustWork = TRUE)
file_prefix <- sub("\\.bed$", "", bed_file)
Genotype <-read_bed(file_prefix)
kin<-Gkin(Genotype)
Results <- IASBLUP(BW56 ~ 1 + Sex + Condition,random = "ID", kinship = kin, max_iter = 20, data = pheno)
This app (IAS-breeding) was built by Wentao Cai(caiwentao@caas.cn). The current release of IAS-breeding contains:
Phenotype summary
Genetic parameters analysis
Calculating breeding values using BLUP, GBLUP
The whole app is deveplotment by {shiny}.
Data visualisation is mainly done with {ggplot2}
IASbreeding shiny web is deployed at http://IASbreeding.cn/ for online use.