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Description
Hello,
I have an issue about the outputs, I already did the DMR calling for all the samples and treatments that I have, I know that I can do more analyses by subsampling from the DMRcalling using the option of reidentify-DMR. But here I have a doubt. When I do the reidentify-DMR in a couple of treatments of interest I can have also the information if they are hyper or hypomethylated but sometimes this information is missing like here
#chr start end number_of_dms hypermethylated_samples hypomethylated_samples
Fvb1 61392 61405 3 RCPCO
Fvb1 231644 231757 3 RMPCO
Fvb1 377565 377649 3 RMPCO
Fvb1 388459 388504 3 RCPCO RMPCO
Fvb1 439936 440166 7 RMPCO
Fvb1 463506 463937 4 RMPCO
Fvb1 497815 498050 3 RMPCO
Fvb1 741828 741834 3 RCPCO RMPCO
Fvb1 792822 792864 4 RMPCO
What does it mean if they are not shown? This I don't understand
As and additional info here is my DMRfind with all the samples
#chr start end number_of_dms hypermethylated_samples hypomethylated_samples methylation_level_RCPCO methylation_level_RMPCO methylation_level_RCPMO methylation_level_RMPMO methylation_level_SCPCO methylation_level_SMPCO methylation_level_SCPMO methylation_level_SMPMO
Fvb1 61392 61405 3 "RCPMO,RCPCO" "SMPCO,SCPMO" 0.3893805309734513 0.24347826086956523 0.4 0.3148148148148148 0.022727272727272728 0.041666666666666664 0.037735849 0.14018691588785046
Fvb1 114263 114745 6 "SCPMO,SMPMO" "RCPCO,SCPCO,RCPMO,RMPCO" 0.4041994750656168 0.42411642411642414 0.3605769230769231 0.5 0.42144638403990026 0.4110429447852761 0.5816326530612245 0.4808080808080808
Fvb1 120031 120068 3 "SMPCO,RCPMO" "SMPMO,SCPCO" 0.7583892617449665 0.6165413533834586 0.7894736842105263 0.7724137931034483 0.5793103448275863 0.8148148148148148 0.6356589147286822 0.673202614
Fvb1 231644 231757 3 RMPCO "SMPCO,SCPCO" 0.7808219178082192 0.8578947368421053 0.7843137254901961 0.6257309941520468 0.5632911392405063 0.46099290780141844 0.6733333333333333 0.7661691542288557
Fvb1 375260 375271 3 "RCPCO,RMPCO" "RMPMO,SMPMO" 0.7319587628865979 0.8205128205128205 0.4175824175824176 0.3333333333333333 0.5865384615384616 0.5783132530120482 0.4852941176470588 0.2785714285714286
Fvb1 377565 377649 3 "RMPCO,RCPMO,SCPCO" "SMPCO,SCPMO" 0.5522388059701493 0.6666666666666666 0.7123287671232876 0.35526315789473684 0.6883116883116883 0.23376623376623376 0.2535211267605634 0.48484848484848486
Fvb1 439936 439989 3 "RMPCO,SCPCO,RCPMO" SMPMO 0.39552238805970147 0.31868131868131866 0.4217687074829932 0.2967032967032967 0.4235294117647059 0.3357664233576642 0.22839506172839505 0.071005917
Fvb1 440132 440166 4 "SCPCO,SMPMO,RMPCO" "RCPMO,SCPMO" 0.3627450980392157 0.4931506849315068 0.10344827586206896 0.20567375886524822 0.4462809917355372 0.3125 0.2608695652173913 0.512396694
Fvb1 449345 449431 4 "RCPMO,SMPCO" "SCPMO,RMPCO" 0.817258883 0.8080808080808081 0.9484536082474226 0.8716981132075472 0.9132231404958677 0.9333333333333333 0.5118110236220472 0.7684210526315789
hope you can help me understand and solve this problem