Subset genes in the initial steps

[camcecc]

Is there a way to subset genes and remove some of them (namely) from the maf file? Or, the opposite, only keep the ones we want to investigate more and would like to see more deeply (i.e. in the oncoprint)? Thanks

[PoisonAlien]

Hi,

Check out filterMaf function. I hope this helps.

#remove genes of intrest
filterMaf(maf = laml, genes =c("TTN", "AHNAK2"))

[camcecc]

Wow that was quick! Thank you so much.

How about selecting genes from the ratio mutation / length? I know this would be MutSig material, but is there a way (maybe simplified) to obtain this data from maftools?

[PoisonAlien]

Hi,

This is a very specific case. But if you know what genes, samples, or genomic regions, you are particularly interested in, you could use subsetMaf.

[camcecc]

I see. Is there some point in the pipeline where I can find the genes length, so I can manually do the ratio and then subset? Thank you again!

[PoisonAlien]

Unfortunately it is not possible :|

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