diff --git a/R/GAPIT.Bus.R b/R/GAPIT.Bus.R index 5aa59bb..5eca1aa 100644 --- a/R/GAPIT.Bus.R +++ b/R/GAPIT.Bus.R @@ -254,10 +254,10 @@ if(n!=num_bins) # print(table(aim_area)) # print(dim(GD)) # aim_area=aim_area[1:(nrow(GWAS))] - # if(setequal(aim_area,logical(0))) next + if(setequal(aim_area,logical(0))) next # this is used to set with sig marker in second model # aim_area[GM[,1]==aim_marker[,1]]=FALSE - secondCV=NULL + # secondCV=NULL secondGD=GD[,c(TRUE,aim_area)] # print(dim(secondGD)) secondGM=GM[aim_area,] @@ -272,7 +272,7 @@ if(n!=num_bins) Second_GWAS= myGAPIT_Second$GWAS [,1:4] Second_GWAS[is.na(Second_GWAS[,4]),4]=1 orignal_GWAS=GWAS[aim_area,] - write.csv(cbind(orignal_GWAS,Second_GWAS),paste("TEST_",i,".csv",sep=""),quote=F) + # write.csv(cbind(orignal_GWAS,Second_GWAS),paste("TEST_",i,".csv",sep=""),quote=F) # GWAS_index=match(Second_GWAS[,1],GWAS[,1]) #test_GWAS=GWAS @@ -317,7 +317,7 @@ if(method=="BlinkC") print("BlinkC will be started !!") colnames(GD)[-1]=as.character(GM[,1]) -# blink_GD=t(GD[,-1]) +blink_GD=t(GD[,-1]) blink_GM=GM blink_Y=Y blink_Y[is.na(blink_Y)]="NaN" @@ -395,8 +395,10 @@ library(biganalytics) #for FARM-CPU #print(head(blink_CV)) # library(BLINK) # source("http://zzlab.net/GAPIT/BLINK.R") - myBlink=Blink(Y=blink_Y,GD=blink_GD,GM=blink_GM,CV=blink_CV,maxLoop=10,time.cal=T,FDRcut=FDRcut) - #print(head(myBlink$GWAS)) + totaltaxa=cbind(blink_Y[,1],GD[,1]) + # print(totaltaxa) + myBlink=Blink(Y=blink_Y,GD=blink_GD,GM=blink_GM,CV=blink_CV,maxLoop=10,cutOff=cutOff,time.cal=T,FDRcut=FDRcut) + # print(head(myBlink$GWAS)) seqQTN=myBlink$seqQTN taxa=names(blink_Y)[2] GWAS=myBlink$GWAS[,1:4] diff --git a/R/GAPIT.MAS.R b/R/GAPIT.MAS.R new file mode 100644 index 0000000..7609eba --- /dev/null +++ b/R/GAPIT.MAS.R @@ -0,0 +1,15 @@ +`GAPIT.MAS` <-function(Y,GD=NULL,GM=NULL,KI=NULL,GWAS=NULL,CM=NULL){ +#Object: Useing MAS to predict phenotype +#Designed by Zhiwu Zhang +#Writen by Jiabo Wang +#Last update: Apr 23, 2021 +############################################################################################## +print("GAPIT.MAS in process...") +#Define the function here + + + + + +} +