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kgori / sigfit

Flexible Bayesian inference of mutational signatures
GNU General Public License v3.0
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Add function to build catalogues #10

Closed baezortega closed 7 years ago

baezortega commented 7 years ago

Incorporate user function to construct the input mutational catalogues from a table with Chrom, Pos, Ref and Alt. We will need to include an extra package like BSgenome.Hsapiens.UCSC.hg19. We should also include the option of using a different genome from a FASTA file (as in SomaticSignatures).

baezortega commented 7 years ago

Working on this now.

kgori commented 7 years ago

Is it possible to do this without adding BSgenome? I'd like to avoid having Bioconductor as a dependency?

baezortega commented 7 years ago

Sure, I'll look into it. I've removed the BSgenome dependency already.

baezortega commented 7 years ago

I haven't found any package that is able to load a whole genome FASTA in a reasonable time and is not part of Bioconductor (although there's surely a way). So far I've made the function so that the user needs to provide a table with REF base, ALT base and trinucleotide context. We can suggest how to obtain the trinucleotide context in the vignettes, or add this later on.