fix table row names

countTable_UTRPolysomes_UTRs_21Nov2017.txt

@@ -35392,6 +35392,6 @@ revgroup01049859	Rbmx	3pUTR_extended	316	3735	469	51	65	44	22	13	18	5	9	102	34	5
 revgroup01049874	Rbmx	3pUTR	346	710	767	52	60	75	43	49	34	13	12	222	70	82	55
 revgroup01049876	Rbmx	3pUTR	374	286	20	3	1	2	0	2	2	2	0	4	2	1	1
 fwdgroup01048965	Bex4	3pUTR	404	137	1493	75	80	270	161	220	231	13	11	208	55	86	83
-<skip>	<skip>	mitochondria	-1	-1	445082	52643	49747	33701	14380	11910	8021	41612	53428	19384	6044	99353	54859
-<skip>	<skip>	intergenic	-1	-1	5914159	625605	753384	823242	526748	383879	355072	113287	175180	831878	284135	559425	482324
-<skip>	<skip>	filtered	-1	-1	1369415	159683	179210	185924	116645	86450	82628	25420	36000	167316	58245	149902	121992
+mitochondria	mitochondria	mitochondria	-1	-1	445082	52643	49747	33701	14380	11910	8021	41612	53428	19384	6044	99353	54859
+intergenic	intergenic	intergenic	-1	-1	5914159	625605	753384	823242	526748	383879	355072	113287	175180	831878	284135	559425	482324
+filtered	filtered	filtered	-1	-1	1369415	159683	179210	185924	116645	86450	82628	25420	36000	167316	58245	149902	121992

edgeR_RUVSeqNorm.R

@@ -12,15 +12,19 @@ library(RUVSeq);
 # clean current variables
 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, check.names=F));
+# read UTR counts
+utrs<-as.matrix(read.table("/Users/tushevg/Desktop/UTRPolyribosomes/countTable_UTRPolysomes_UTRs_21Nov2017.txt",stringsAsFactors=F, header=T, row.names=1, check.names=F));
+
+
+# read ERCC counts
+ercc<-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")];
+#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,];
+#filter<-apply(data, 1, function(x) length(x[x>5]) >= 2);
+#filtered<-data[filter,];