new.hgvs.builder.c: Coding Sequence HGVS Builder

In jweile/hgvsParseR: Parse HGVS variant descriptor strings

Description

A constructor for a CDS (=coding sequence) HGVS builder object. The object contains a collection of functions for building CDS HGVS strings. The resulting object encapsulates the following functions:

• substitution(pos,ancestral,variant,posOffset=0) CDS substitution variants. pos = position (integer); ancestral = ancestral nucleotide [ACGT]; variant = variant nucleotide [ACGT]; posOffset = offset from the position when crossing exon-intron borders (integer, defaults to 0)

• deletion(start,stop,startOffset=0,stopOffset=0) CDS deletion. start = start position (integer); stop = stop position (integer); startOffset = offset from the start position when crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the stop position when crossing exon-intron borders (integer, defaults to 0)

• inversion(start,stop,startOffset=0,stopOffset=0) CDS inversion. start = start position (integer); stop = stop position (integer); startOffset = offset from the start position when crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the stop position when crossing exon-intron borders (integer, defaults to 0)

• duplication(start,stop,startOffset=0,stopOffset=0) CDS duplication. start = start position (integer); stop = stop position (integer); startOffset = offset from the start position when crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the stop position when crossing exon-intron borders (integer, defaults to 0)

• insertion(start,variant,startOffset=0) CDS insertion. start = position immediately preceeding the insertion (integer); seq = inserted nucleotide sequence [ACGT]+ ; startOffset = offset from the start position when crossing exon-intron borders (integer, defaults to 0)

• delins(start,stop,variant,startOffset=0,stopOffset=0) CDS deletion and insertion. start = start position (integer); stop = stop position relative to the reference (integer); seq = inserted nucleotide sequence [ACGT]+ ; startOffset = offset from the start position when crossing exon-intron borders (integer, defaults to 0); stopOffset = offset from the stop position when crossing exon-intron borders (integer, defaults to 0)

• cis(...) Multi-variant phased in cis. Parameters are coding HGVS strings for the corresponding single mutants

• trans(...) Multi-variant phased in trans. Parameters are coding HGVS strings for the corresponding single mutants

• nophase(...) Multi-variant with unknown phasing. Parameters are coding HGVS strings for the corresponding single mutants

Usage

new.hgvs.builder.c()

Value

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

Examples

builder <- new.hgvs.builder.c()
string1 <- builder$substitution(123,"A","G",posOffset=2)
string2 <- builder$delins(123,129,"ATTG")
string3 <- with(builder,cis(substitution(123,"A","C"),substitution(231,"G","A")))

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