Map from mutation type (aka, variant classification) to mutation class. Default mappings are as follows,
Missense
Missense_Mutation --- the point mutation alters the protein structure by one amino acid. See https://en.wikipedia.org/wiki/Missense_mutation.
Inframe
In_Frame_Del --- deletion that keeps the sequence in frame
In_Frame_Ins --- insertion that keeps the sequence in frame
Silent --- variant is in coding region of the chosen transcript, but protein structure is identical (i.e., a synonymous mutation)
Targeted_Region --- targeted region
Truncating
Frame_Shift_Ins --- insertion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.
Frame_Shift_Del --- deletion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.
Nonsense_Mutation --- a premature stop codon is created by the variant. See https://en.wikipedia.org/wiki/Nonsense_mutation.
Nonstop_Mutation --- variant removes stop codon.
Splice_Site --- the variant is within two bases of a splice site.
Splice_Region --- the variant is within splice region.
Other
5'UTR --- variant is on the 5'UTR for the chosen transcript
3'UTR --- variant is on the 3'UTR for the chosen transcript
5'Flank --- the variant is upstream of the chosen transcript (within 3kb)
3'Flank --- the variant is downstream of the chosen transcript (within 3kb)
Fusion --- gene fusion
IGR --- intergenic region. Does not overlap any transcript.
Intron --- variant lies between exons within the bounds of the chosen transcript.
Translation_Start_Site --- variant in translation start site.
De_novo_Start_InFrame --- New start codon is created by the given variant using the chosen transcript. However, it is in frame relative to the coded protein.
De_novo_Start_OutOfFrame --- New start codon is created by the given variant using the chosen transcript. However, it is out of frame relative to the coded protein.
Start_Codon_SNP --- point mutation that overlaps the start codon.
Start_Codon_Ins --- insertion that overlaps the start codon.
Start_Codon_Del --- selection that overlaps the start codon.
RNA --- variant lies on one of the RNA transcripts.
lincRNA --- variant lies on one of the lincRNAs.
Unknown --- Unknown
mapMutationTypeToMutationClass(mutation.type.vec,
mutation.type.to.class.df = NA)a vector of mutation type information
A mapping table from mutation type (header Mutation_Type)
to mutation class (header Mutation_Class).
Default NA, which indicates to use default mappings.
a vector of mapped mutation class information