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

In g3viz: Interactively Visualize Genetic Mutation Data using a Lollipop-Diagram

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
)

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.

Value

a vector of mapped mutation class information

g3viz documentation built on Sept. 11, 2024, 9:25 p.m.