Hi everyone,

I am using bumphunter function from minfi package for patients (Healthy donors and treatments ) dataset to find DMRs. Where i design contrasts based on the patient's methylation level at different time points and got the tables from the result, you could see below. I don't understand why the bumphunter function chooses only one cluster from my dataset?

If anyone has a suggestion, that will also help me.

Thanks

HD2_0vs22h_0ng <- as.factor( c("HD2.0h.0ng", "HD2.22h.0ng")) 

Mm_HD2_0vs22h_0ng <- model.matrix(~HD2_0vs22h_0ng) # The design matrix

Bumps1 <- minfi::bumphunter(NTFlt[ ,c(30,34)], design = Mm_HD2_0vs22h_0ng, cutoff = c(-3,3), cluster= Clus_chr_table,                        B=100,type="M") 

head(bumpsTable1, n=10)

     X   chr     start       end     value     area   cluster indexStart indexEnd L clusterL     p.value fwer p.valueArea fwerArea

1   88  chrX   9433103   9433103       Inf      Inf   chrX109     580719   580719 1       24 0.003787879    1 0.003787879        1

2  262  chrX  18710913  18710913 -9.960673 9.960673   chrX315     581913   581913 1       24 0.007575758    1 0.007575758        1

3   69  chr6  28832727  28832727  8.684412 8.684412  chr61606     200437   200437 1       80 0.011363636    1 0.011363636        1

4  236  chr7  73039066  73039066 -8.394728 8.394728  chr73120     244901   244901 1       12 0.015151515    1 0.015151515        1

5   44  chr2 233323935 233323935  8.253298 8.253298  chr29629      97745    97745 1       18 0.018939394    1 0.018939394        1

6   80  chr7  87105216  87105216  8.114027 8.114027  chr73692     246992   246992 1       17 0.022727273    1 0.022727273        1

7  136 chr14  23504247  23504247 -7.774084 7.774084  chr14203     415120   415120 1       20 0.026515152    1 0.026515152        1

8   26 chr17  41132655  41132655  7.622053 7.622053 chr173062     493947   493947 1       14 0.030303030    1 0.030303030        1

9  243  chr7 149420655 149420655 -7.207667 7.207667  chr76407     258182   258182 1       19 0.034090909    1 0.034090909        1

10 180 chr22  21305099  21305099 -7.159384 7.159384  chr22362     569434   569434 1        3 0.037878788    1 0.037878788        1