How to smooth methylation data

Question

[chaudharyc61]

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

Answer 1

[German.M.Demidov]

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.