AFEchidna包可以运行同种非正态分布变量的批量分析,简单示例如下:
res21<-echidna(es0.file="dfm2.es0",
trait=~dis+lt,
fixed=~1+Rep,
random=~Mum,
family=esr_binomial(),
batch=T)
运行结果如下:
> res21<-echidna(es0.file="dfm2.es0",
+ trait=~dis+lt,
+ fixed=~1+Rep,
+ random=~Mum,
+ family=esr_binomial(),
+ batch=T)
Program starts running batch analysis ------
run dis -- -- --:
Running Echidna for analysis: dis
Wed Aug 11 22:40:17 2021
Iteration LogL eSigma NEDF
1 1 -424.14 0.9763 554
2 2 -421.41 0.9800 554
3 3 -418.93 0.9858 554
4 4 -418.98 0.9855 554
5 5 -418.99 0.9855 554
6 6 -418.99 0.9855 554
Wed Aug 11 22:40:18 2021 LogL Converged
run lt -- -- --:
Running Echidna for analysis: lt
Wed Aug 11 22:40:18 2021
Iteration LogL eSigma NEDF
1 1 -424.77 0.9764 554
2 2 -419.40 0.9841 554
3 3 -420.20 0.9821 554
4 4 -420.22 0.9821 554
5 5 -420.22 0.9821 554
Wed Aug 11 22:40:19 2021 LogL Converged
> res21b<-b2s(res21)
> lapply(res21b, Var)
$`dis `
Term Sigma SE Z.ratio
1 Residual 0.985460 0.062299 15.818231
2 Mum 0.048413 0.040492 1.195619
$` lt`
Term Sigma SE Z.ratio
1 Residual 0.982100 0.061909 15.863606
2 Mum 0.058509 0.041182 1.420742
AFEchidna包免费对外开放,仅用于学术研究,不可用于商业研究,否则造成的后果自负。
感兴趣者,可发邮件到yzhlinscau@163.com免费索取程序包。
参考文献:
Zhang WH, Wei RY, Liu Y, Lin YZ. AFEchidna is a R package for genetic evaluation of plant and animal breeding datasets. BioRxiv. DOI: 10.1101/2021.06.24.449740.