setwd('D:/brca')

library('imputeMissings')

data=read.csv("brca_multitest.csv",row.names = 1)

#################delete missing#######################

sum(is.na(data))

miss=c()

for (i in 1:nrow(data)){

  miss=c(miss,sum(is.na(data[i,])))

}

missrate=miss/ncol(data)

data1=data[missrate<0.2,]

data1[is.na(data1)] <- 0

###################delete zero#################

nz=c()

for (i in 1:nrow(data1)){

  nz=c(nz,sum(data1[i,]==0))

}

zerorate=nz/ncol(data1)

data2=data1[zerorate<0.2,]

###############impute######################

data3=t(data2)

data3=data.frame(data3)

data3[data3==0]=NA

data4<-impute(data3)

##########normalize##############

data5=t(data4)

data6=data5

data7=t(data6)

data8=scale(data7, center = T, scale = T)

data9=t(data8)

write.csv(data9,'brcatest_go.csv')