Create text binary matrix which retains specific mutation type in matrix

[karissawhiting]

@edrill suggested this. This can be useful for oncoprints and more in-depth mutation specific analyses.

The relevant information seems to be in the following MAF columns:

table(gnomeR::mutations$mutationType, gnomeR::mutations$variantType)
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2
#>                         
#>                          DEL DNP INS ONP SNP
#>   Frame_Shift_Del         89   0   0   0   0
#>   Frame_Shift_Ins          0   0  38   0   0
#>   In_Frame_Del            23   0   0   0   0
#>   Missense_Mutation        0   5   0   0 479
#>   Nonsense_Mutation        0   1   1   0  57
#>   Nonstop_Mutation         0   0   0   1   0
#>   Splice_Site              6   0   0   0  24
#>   Translation_Start_Site   0   0   0   0   1

@edrill - what type of information from the above do you maintain in your matrix? Also, does this only apply to mutations or fusions/CNA as well?

@michaelcurry1123 - I'm thinking this could be a separate new function that doesn't rely on the other version of the binary matrix, but I'm open to other ideas. Not sure what to call it yet. I think we should add a check of possible levels (e.g. missense, splice, etc...)