Nothing
getGenos<-function(genDatabase,IDs=NULL,markerNames=NULL,minMAF=0,maxFreqNA=1,na.code=9,addColnames=TRUE,addRownames=TRUE)
{
MAP<-read.table(file=paste(genDatabase,'/binary/map.txt',sep=''),header=TRUE)
p<-ifelse(is.null(markerNames),nrow(MAP),length(whichMarkers))
if(is.null(markerNames)){
keepMarker<-rep(TRUE,p)
}else{
keepMarker<-MAP$rs%in%markerNames
}
tmp<-(MAP$freqNAs>=(1-maxFreqNA))
keepMarker<-keepMarker&tmp
MAF=ifelse(MAP$freqAleleOne>0.5,1-MAP$freqAleleOne,MAP$freqAleleOne)
tmp<-MAF>=minMAF
keepMarker<-keepMarker&tmp
whichMarkers<-which(keepMarker)
if(length(whichMarkers)==0){ stop('No marker satisfied the required MAF and frequ of NA conditions') }
filein<-paste(genDatabase,'/binary/genosInt.bin',sep='')
IDsDB<-scan(paste(genDatabase,'/binary/IDs.txt',sep=''),what=character(),quiet=TRUE)
if(is.null(IDs)){IDs<-IDsDB }
tmp<-IDs%in%IDsDB
if(sum(tmp)==0){
stop('None of the IDs exist in the database')
}else{
if(sum(tmp)<length(IDs)){
print(paste('Warning, only ', sum(tmp), ' out of the ', length(IDs), ' IDs appear in the database',sep=''))
}
}
IDs<-IDs[which(tmp)]
n<-length(IDs)
X<-matrix(nrow=n,ncol=length(whichMarkers),NA)
if(addRownames){ rownames(X)<-IDs }
if(addColnames){ colnames(X)<-MAP$rs[whichMarkers] }
cat("\n################################################## 100%% \n");
for(i in 1:n)
{
#tmp<-i%in%seq(from=1,to=n,by=100)
#if(tmp)
#{
# cat('Loading genotype ',i,' (',round(100*i/n),'%)',sep='');cat('\n')
#}
tmp<-which(IDsDB==IDs[i])
tmp<-readBinGenInt( filename=filein,p=p,whichGenotype=tmp)
tmp<-tmp[whichMarkers]
tmp<-ifelse(tmp==na.code,NA,tmp)
X[i,]<-tmp
progress1<-as.integer(i/n*100);
progress2<-as.integer((i+1)/n*100)
if(progress1%%2==0)
{
if(progress2%%2!=0) cat("#");
}
}
cat("\n")
return(X)
}
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