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')