> library("edgeR")
Loading required package: limma
> a<-read.delim("C:\\100bp50offsetcountcolmockvsfox1DPI.txt",row.name=1,TRUE)
> head(a)
         S1 S2 S5 S6
Chr1:1   86 49 56 40
Chr1:51  42 30 39 31
Chr1:101  4  7  3  3
Chr1:151  0  2  1  2
Chr1:201  1  0  1  4
Chr1:251 32 25 17 18
> group<-factor(c(1,1,2,2))
> b<-DGEList(counts=1, group=group)
Error in DGEList(counts = 1, group = group) : 
  Length of 'group' must equal number of columns in 'counts'
> b<-DGEList(counts=a, group=group)
> dim(b)
[1] 2393345       4
> keep<-rowSums(cpm(b)>1)>=2
> b<-b[keep,]
> dim(b)
[1] 77811     4
> b$samplesSlib.size<-colSums(b$counts)
> b<-calcNormFactors(b)
> b$samples
   group lib.size norm.factors
S1     1 18148268    1.0931307
S2     1 17169871    1.0974397
S5     2 16812419    0.9413272
S6     2 17653722    0.8855368
> b<-estimateCommonDisp(b,verbose=TRUE)
Disp = 0.00703 , BCV = 0.0839 
> b<-estimateTagwiseDisp(b)
> top<-topTags(et)
> et<-exactTest(b)
> topTags(et)
Comparison of groups:  2-1 
               logFC   logCPM        PValue           FDR
ChrC:651    3.143491 6.489829 1.577953e-126 1.227821e-121
ChrC:137501 2.899128 7.144442 1.286869e-114 5.006629e-110
ChrC:701    3.019486 5.973865 2.110958e-113 5.475191e-109
ChrC:136701 2.699085 6.399060 6.388976e-109 1.242831e-104
ChrC:131801 2.709633 6.453667 1.179523e-107 1.835597e-103
ChrC:106701 2.717326 6.678797 1.312477e-106 1.702086e-102
ChrC:1351   2.936272 5.621700 3.739849e-101  4.157163e-97
ChrC:101051 2.920198 7.183182 1.384538e-100  1.346654e-96
ChrC:105501 2.665605 6.172738 2.665146e-100  2.304196e-96
ChrC:131851 2.775614 6.647464  1.048855e-99  8.161246e-96
> detags<-rownames(topTags(et))
> cpm(b)[detags,]
                  S1       S2        S5        S6
ChrC:651    17.64253 18.89306 152.59712 170.28059
ChrC:137501 34.22650 32.63829 232.33938 266.61514
ChrC:701    13.20669 14.38208 106.34408 117.37975
ChrC:136701 22.88488 22.13035 140.90748 151.53821
ChrC:131801 23.74180 22.71413 145.70971 158.31873
ChrC:106701 27.52234 26.53520 167.38292 188.25536
ChrC:1351   11.84570 10.87943  82.20656  91.92081
ChrC:101051 36.79727 30.99311 241.05921 272.37218
ChrC:105501 20.56614 18.68078 120.62439 128.57400
ChrC:131851 27.06867 23.98782 165.67687 184.16147
> summary(de<-decideTestsDGE(et))
   [,1] 
-1   213
0  75809
1   1789
> detags<-rownames(b)[as.logical(de)]
> top<-topTags(et,77811)
> write.csv(top$table,file="noDEedgeR2.csv"
+ )
> detags<-rownames(topTags(et,77811))
> detag2<-cpm(b)[detags,]
> write.table(detag2,file="noDEdetag2.csv",sep=",")
>