Finding standard deviation from dataframe
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5 weeks ago
soyeon • 0

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Hi,

I'm studying about DNA methylation.

I ran minfi to get a beta value file, but the file size is too large.

So i have to filtering this file as standard deviation >0.05 by cgIDs.

How do I get standard deviation value??

standard DNAmethylation deviation • 179 views
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I am not convinced about filtering CpGs by standard deviation because "the file is too large" but if you want to do that using R, you can use apply(dataframe,1,sd) to obtain sd for each CpG

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Thank you so much...

Do you know how to get the standard deviation of rows all at once and add them to the dataframe?

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Supposing df is your dataframe of beta values : df$sd = apply(df,1,sd)

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