How to smooth methylation data
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Entering edit mode
2.8 years ago
chaudharyc61 ▴ 80

Hello Everyone

I have a TAB delimited file having details as

Chr     Window_start      Window_end      Mutant_Meth_score         Wild_Meth_score      log2(Wild_Meth_score/Wild_Meth_score)

I want to smooth the Log2 value so that i can easily use it to plot in R using plot function. Can anyone tell me how can i do it as in between my data there are some outliers because of that i can't directly plot them.

I thought of using filter function from stats package but i have no idea what parameters i should use and also what should be given to filter parameter.

Thanks in advance. Chandan Kumar

Bisulfite-seq Analysis • 462 views
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Entering edit mode
2.8 years ago

There are many papers that use smoothing as a first step of their approach, such as: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2012-13-10-r83 , I think you may check which approach they have applied.

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