new.hgvs.builder.g: Genomic HGVS Builder
In jweile/hgvsParseR: Parse HGVS variant descriptor strings

Description Usage Details Value Examples

View source: R/buildHGVS.R

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

1	new.hgvs.builder.g()

The resulting object encapsulates the following functions:

substitution(pos,ancestral,variant) Genomic substitution variants. pos = position (integer); ancestral = ancestral nucleotide [ACGT]; variant = variant nucleotide [ACGT]
deletion(start,stop) Genomic deletion. start = start position (integer); stop = stop position (integer)
inversion(start,stop) Genomic inversion. start = start position (integer); stop = stop position (integer)
duplication(start,stop) Genomic duplication. start = start position (integer); stop = stop position (integer)
insertion(start,variant) Genomic insertion. start = position immediately preceeding the insertion (integer); seq = inserted nucleotide sequence [ACGT]+
delins(start,stop,variant) Genomic deletion and insertion. start = start position (integer); stop = stop position relative to the reference (integer); seq = inserted nucleotide sequence [ACGT]+
cis(...) Multi-variant phased in cis. Parameters are genomic HGVS strings for the corresponding single mutants
trans(...) Multi-variant phased in trans. Parameters are genomic HGVS strings for the corresponding single mutants
nophase(...) Multi-variant with unknown phasing. Parameters are genomic HGVS strings for the corresponding single mutants

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

builder <- new.hgvs.builder.g()
string1 <- builder$substitution(123,"A","G")
string2 <- builder$delins(123,129,"ATTG")
string3 <- with(builder,cis(substitution(123,"A","C"),substitution(231,"G","A")))