Question: How to smooth methylation data
0
gravatar for chaudharyc61
12 days ago by
chaudharyc6120
India
chaudharyc6120 wrote:

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 • 57 views
ADD COMMENTlink modified 9 days ago by Kevin Blighe54k • written 12 days ago by chaudharyc6120
1
gravatar for German.M.Demidov
12 days ago by
Tübingen
German.M.Demidov1.5k wrote:

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.

ADD COMMENTlink written 12 days ago by German.M.Demidov1.5k
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