I would like to create a maf file from a variants data.frame, which uses different variant classes than those used by read.maf.
I have tried to map the variant classification classes in my data to those of MAFtools, but could not manage to map all variant classes. I am a student for bioinformatics with little molecular biology expertise. A google search could not give me clear guidance as how to proceed.
I would appreciate any help with mapping the following variants:
non_coding_exonic, non_coding_intronic, upstream_gene, 5_prime_UTR_intronic, kozak_sequence, downstream_gene, stop_gained, stop_retained, initiator_codon, 3_prime_UTR_intronic, stop_lost
... to the variants classes required by MAFtools:
Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Translation_Start_Site, Nonstop_Mutation, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR, Intron, RNA, Targeted_Region
Thanks very much.