resort data

edgeR_RUVSeqNorm.R

@@ -13,7 +13,14 @@ library(RUVSeq);
 rm(list = ls());
 
 # read counts
-indata<-as.matrix(read.table("/Users/tushevg/Desktop/UTRPolyribosomes/countTable_UTRPolysomes_ERCC_21Nov2017.txt",stringsAsFactors=F, header=T, row.names=1));
+indata<-as.matrix(read.table("/Users/tushevg/Desktop/UTRPolyribosomes/countTable_UTRPolysomes_ERCC_21Nov2017.txt",stringsAsFactors=F, header=T, row.names=1, check.names=F));
+
+# reorder data by name
+data<-indata[,c("InputHc2","InputHc3","80SHc2","80SHc3","2and3Hc2","2and3Hc3","4and5Hc2","4and5Hc3","6and7Hc2","6and7Hc3","bigger7Hc2","bigger7Hc3")];
+
+# filter data
+filter<-apply(data, 1, function(x) length(x[x>5]) >= 2);
+filtered<-data[filter,];