A single nucleotide variation

This function creates SNVs and indels.

Arguments

chr

The name of the chromosome in which the indel occurs.

chr_pos

The position in the chromosome where the indel occurs.

ref

The reference sequence.

alt

The mutation altered sequence.

allele

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

cause

The cause of the mutation (optional).

Details

It generalizes the function SNV() by building SNVs and indels. However, it requires the reference sequence specification whereas SNV() can deduce it from the reference sequence itself.

Another difference with respect to SNV() is the ref-alt parameter order: the alt parameter comes before the optional ref parameter in SNV(); Mutation() adopts the reverse order.

See also

SNV() for SNV creation.

Examples

# create a deletion without specifying the cause
mutation <- Mutation("X", 20002, "TAC", "T")
mutation
#> indel(chr: X, chr_pos: 20002, allele: random, ref: TAC, alt: T)

# create an insertion and do not specify the cause
mutation <- Mutation("X", 20002, "A", "AT")
mutation
#> indel(chr: X, chr_pos: 20002, allele: random, ref: A, alt: AT)

# create an insertion that must be place in allele 1
mutation <- Mutation("X", 20002, "A", "AT", allele = 1)
mutation
#> indel(chr: X, chr_pos: 20002, allele: 1, ref: A, alt: AT)

# create an insertion with a cause
mutation <- Mutation("X", 20002, "A", "AT", cause = "SBS1")
mutation
#> indel(chr: X, chr_pos: 20002, allele: random, ref: A, alt: AT, cause: "SBS1")