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hhg7 / defiant

Differential methylation: Easy, Fast, Identification and ANnoTation
GNU General Public License v2.0
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Difference Methylation analysis on Regions Of Interesting (ROI) #1

Closed ChengYunazhi closed 6 years ago

ChengYunazhi commented 6 years ago

Hi, 

can defiant analysis Difference Methylation on ROI？For example, I want to analysis difference methylation of a set of immune response genes between two groups,  the difference methylation is on whole genebody level, not DMR.

Thanks!

Yuanzhi

hhg7 commented 6 years ago

hi @ChengYunazhi Defiant was designed to identify differentially methylated regions. However, you can run defiant with the "-E" option to get information about every CpG/CpN site and compare on a whole genebody level as you want. This will give you a p-value and percent difference for every CpG/CpN site in a file that starts with "nucleotide". You can compare different regions this way. You can paste attach the output file here, if you like, and I can help.

ChengYunazhi commented 6 years ago

Thanks David, I'll try this "-E" option.

ChengYunazhi commented 6 years ago

Hi, @hhg7

Is there a statistical method that gives just one p-value for differential methylation of ROIs? I used defiant to get a p-value for ever CpG in ROIs, but how to assess whether there is a significant difference in mean methylation level between the two sample or two groups in these ROIs? A similar analysis can be done in the MEDIP-seq data, I don’t know if this method is feasible in WGBS data?

Thanks

Yuanzhi

hhg7 commented 6 years ago

hi @ChengYunazhi I will write a script to do what you ask, it might be a few days. It will process the output file from the "-E" option.

ChengYunazhi commented 6 years ago

Thanks for your kind help, @hhg7 . Is it possible to have the method address datasets with or without biological replicates?

hhg7 commented 6 years ago

hi @ChengYunazhi yes, if there are no biological replicates the program uses Fisher's exact test instead of Welch's t-test.

hhg7 commented 6 years ago

@ChengYunazhi I've uploaded the program roi.c onto the main repository. Please let me know how it runs. I look forward to your response.

ChengYunazhi commented 6 years ago

Thanks @hhg7 , I will run it and give you feedback !

hhg7 commented 6 years ago

@ChengYunazhi did the roi program do what you intended? please let me know, I'd like to close the issue.