g3viz (version 1.2.0)

mapMutationTypeToMutationClass: Map from mutation type (aka, variant classification) to mutation class

Description

Map from mutation type (aka, variant classification) to mutation class. Default mappings are as follows,

• Missense

  • Missense_Mutation --- a point mutation in which a single nucleotide change results in a codon that codes for a different amino acid See https://en.wikipedia.org/wiki/Missense_mutation.

• Inframe

  • In_Frame_Del --- a deletion that keeps the sequence in frame

  • In_Frame_Ins --- an 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 --- a variant caused by indels of a number of nucleotides in a DNA sequence that is not divisible by three. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Frame_Shift_Ins --- a variant caused by insertion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Frame_Shift_Del --- a variant caused by deletion that moves the coding sequence out of frame. See https://en.wikipedia.org/wiki/Frameshift_mutation.

  • Nonsense_Mutation --- a premature stop codon that is created by the variant. See https://en.wikipedia.org/wiki/Nonsense_mutation.

  • Nonstop_Mutation --- a variant that removes stop codon.

  • Splice_Site --- a variant that is within two bases of a splice site.

  • Splice_Region --- a variant that is within splice region.

• Other

  • 5'UTR --- a variant that is on the 5'UTR for the chosen transcript.

  • 3'UTR --- a variant that is on the 3'UTR for the chosen transcript.

  • 5'Flank --- a variant that is upstream of the chosen transcript (generally within 3kb).

  • 3'Flank --- a variant that is downstream of the chosen transcript (generally within 3kb).

  • Fusion --- a gene fusion.

  • IGR --- an intergenic region. Does not overlap any transcript.

  • Intron --- a variant that lies between exons within the bounds of the chosen transcript.

  • Translation_Start_Site --- a variant that is in translation start site.

  • De_novo_Start_InFrame --- a novel start codon that is created by the given variant using the chosen transcript. However, it is in frame relative to the coded protein.

  • De_novo_Start_OutOfFrame --- a novel start codon that is created by the given variant using the chosen transcript. However, it is out of frame relative to the coded protein.

  • Start_Codon_SNP --- a point mutation that overlaps the start codon.

  • Start_Codon_Ins --- an insertion that overlaps the start codon.

  • Start_Codon_Del --- a deletion that overlaps the start codon.

  • RNA --- a variant that lies on one of the RNA transcripts.

  • lincRNA --- a variant that lies on one of the lincRNAs.

  • Unknown --- Unknown

Usage

mapMutationTypeToMutationClass(
  mutation.type.vec,
  mutation.type.to.class.df = NA
)

Value

a vector of mapped mutation class information

Arguments

mutation.type.vec

a vector of mutation type information

mutation.type.to.class.df

A mapping table from mutation type (header Mutation_Type) to mutation class (header Mutation_Class). Default NA, which indicates to use default mappings.