new.hgvs.builder.p: Protein HGVS Builder

In jweile/hgvsParseR: Parse HGVS variant descriptor strings

Description

A constructor for a protein-level HGVS builder object. The object contains a collection of functions for building protein HGVS strings.

Usage

new.hgvs.builder.p(aacode = c(1, 3))

Details

The resulting object encapsulates the following functions:

• synonymous() A synonymous variant. No parameters required.

• synonymous(pos,ancestral) Unofficial (yet frequently used) version of synonymous variant syntax. pos = position (integer); ancestral = ancestral amino acid in one-letter or three-letter code.

• substitution(pos,ancestral,variant) AA substitution variants. pos = position (integer); ancestral = ancestral amino acid in one-letter or three-letter code; variant = variant amino acid in one-letter or three-letter code

• deletion(startPos,startAA,endPos,endAA) AA deletion. startPos = start position (integer); startAA = start amino acid in one-letter or three-letter code; endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code

• duplication(startPos,startAA,endPos,endAA) AA duplication. startPos = start position (integer); startAA = start amino acid in one-letter or three-letter code; endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code

• insertion(leftPos,leftAA,rightAA,seq) AA insertion. leftPos = position immediately preceeding the insertion (integer); leftAA = corresponding amino acid in one-letter or three-letter code; rightAA = amino acid to the right of the insertion, in one-letter or three-letter code; seq = inserted amino acid sequence, given as a character vector containing the individual one-letter or three-letter amino acid codes.

• delins(startPos,startAA,endPos,endAA,seq) AA deletion and insertion. startPos = start position (integer); startAA = start amino acid in one-letter or three-letter code; endPos = stop position (integer); endAA = start amino acid in one-letter or three-letter code; seq = inserted amino acid sequence, given as a character vector containing the individual one-letter or three-letter amino acid codes.

• frameshift(startPos,startAA,variantAA=NA,newStop=NA) Frameshift variant. startPos = start position (integer); startAA = start amino acid in one-letter or three-letter code; variantAA = amino acid replacing the start position in the frameshift sequence, given in one-letter or three-letter code, or NA to omit (default); newStop = the position of the nearest coding resulting from the frameshift, or NA to omit (default).

• cis(...) Multi-variant phased in cis. Parameters are coding HGVS strings for the corresponding single mutants. As phasing in trans would be nonsensical in a protein context, the trans() and nophase() methods are not provided here.

Value

A hgvs.builder.g object with functions for building genomic HGVS strings. The individual functions return single-element character vectors containing these strings.

Examples

builder <- new.hgvs.builder.g()
string1 <- builder$substitution(123,"R","K")
string2 <- builder$delins(123,"Arg",152,"Leu",c("Lys","Trp","Ser"))
string3 <- with(builder,cis(substitution(123,"R","K"),deletion(125,"S",152,"L")))

jweile/hgvsParseR documentation built on Sept. 14, 2021, 10:45 p.m.