Creating a SNV

This function creates SNVs.

Arguments

chr

The name of the chromosome in which the SNV occurs.

chr_pos

The position in the chromosome where the SNV occurs.

alt

The base after the mutation.

ref

The base before the mutation (optional).

allele

The allele in which the SNV must occur (optional).

cause

The cause of the SNV (optional).

See also

Mutation() for SNV and indel creation.

Examples

# create a SNV without specifying the cause and context
snv <- SNV("X", 20002, "T")
snv
#> SNV(chr: X, chr_pos: 20002, allele: random, ref: ?, alt: T)

# create a SNV and do not specify the cause
snv <- SNV("X", 20002, "T", "A")
snv
#> SNV(chr: X, chr_pos: 20002, allele: random, ref: A, alt: T)

# create a SNV that must be place in allele 1
snv <- SNV("X", 20002, "T", allele = 1)
snv
#> SNV(chr: X, chr_pos: 20002, allele: 1, ref: ?, alt: T)

# create a SNV with a cause
snv <- SNV("X", 20002, "T", cause = "SBS1")
snv
#> SNV(chr: X, chr_pos: 20002, allele: random, ref: ?, alt: T, cause: "SBS1")