diff --git a/README.md b/README.md index 3682acc..cd6da0b 100644 --- a/README.md +++ b/README.md @@ -33,7 +33,8 @@ Gbye main package, coordinate other function packages for GWAS and GS operations ***Quantile-Quantile Plots***
![QQ Plot by demo data](https://raw.githubusercontent.com/liu-xinrui/GbyE/main/base/QQplot.jpg)
-# **How to use** +# **Analysis** +## **Example** ``` #Loading support packages source("https://raw.githubusercontent.com/liu-xinrui/GbyE/main/GbyE.R") @@ -50,12 +51,56 @@ Y=Y[match(GD[,1],Y[,1]),] #Run GbyE myGbyE=GbyE(GD=GD, - GM=GM,Y=Y, - PCA.total=3, - gwas=F,gs=T, - plot=T, - gwas.model="MLM", - method="gapit") + GM=GM, + Y=Y, + PCA.total=3, + gwas=T, + gs=T, + plot=T, + gwas.model="MLM", + method="gapit") +``` +## **GWAS** +``` +#GAPIT-" MLM" " CMLM" ,"BLINK" "FramCPU" "SUPER" etc +GbyE_GWAS=GbyE(GD=GD, + GM=GM, + Y=Y, + PCA.total=3, + gwas=T, + plot=T, + gwas.model=c("MLM","CMLM","BLINK","FramCPU","SUPER")) +``` +## **GS** +### **rrBLUP** +``` +#Support all rrblup built-in methods +GbyE_GS_rrBLUP=GbyE(GD=GD, + GM=GM, + Y=Y, + gs=T, + method="rrblup", + gs.model="ML") +``` +### **GAPIT** +``` +#Support all GAPIT built-in methods +GbyE_GS_GAPIT=GbyE(GD=GD, + GM=GM, + Y=Y, + gs=T, + method="gapit", + gs.model=c("gBLUP","MABLUP","cBLUP","sBLUP")) +``` +### **BGLR** +``` +#Support all rrblup built-in methods +GbyE_GS_BGLR=GbyE(GD=GD, + GM=GM, + Y=Y, + gs=T, + method="bglr", + gs.model="RRB") #BL BA BB BC RRB etc ``` # **Improve GbyE's test function package**