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im3sanger / dndscv

dN/dS methods to quantify selection in cancer and somatic evolution
GNU General Public License v3.0
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Undefined column in running dndscv #26

Closed beginner984 closed 5 years ago

beginner984 commented 5 years ago

Sorry,

This command always returns error

signif_genes = sel_cv[sel_cv$qglobal_cv<0.1, c("gene_name","qglobal_cv")] Error in [.data.frame(sel_cv, sel_cv$qglobal_cv < 0.1, c("gene_name", : undefined columns selected

im3sanger commented 5 years ago

Hello,

I suspect that the reason for this is that you are not using indels in this analysis (or that you do not have enough of them to trigger the use of the indel model).

The key sentence in the tutorial is this one:

The global q-value integrating all mutation types are available in the qglobal_cv and qallsubs_cv columns for analyses with and without indels, respectively.

So, instead of the line above, you need to use: signif_genes = sel_cv[sel_cv$qglobal_cv<0.1, c("gene_name","qallsubs_cv")]

beginner984 commented 5 years ago

Thanks a lot,

You absolutely right because I am analysing SNV and indel files separately. So may I must combine them

Thank you for being very responding