Construct necessary information for insertions and deletions (indels) that will
be used in `create_variants`

.

indels(rate, max_length = 10, a = NULL, rel_rates = NULL)

rate | Single number specifying the overall indel rate among all lengths. |
---|---|

max_length | Maximum length of indels. Defaults to |

a | Extra parameter necessary for generating rates from a Lavalette distribution.
See Details for more info. Defaults to |

rel_rates | A numeric vector of relative rates for each indel length
from 1 to the maximum length.
If provided, all arguments other than |

An `indel_rates`

object, which is just a wrapper around a numeric vector.
You can access the rates vector for `indel_rates`

object `x`

by running
`as.numeric(x)`

.

Both insertions and deletions require the `rate`

parameter, which specifies
the overall insertion/deletion rate among all lengths.
The `rate`

parameter is ultimately combined with a vector of relative rates among
the different lengths of insertions/deletions from 1 to the maximum
possible length.
There are three different ways to specify/generate relative-rate values.

Assume that rates are proportional to

`exp(-L)`

for indel length`L`

from 1 to the maximum length (Albers et al. 2011). This method will be used if the following arguments are provided:`rate`

`max_length`

Generate relative rates from a Lavalette distribution (Fletcher and Yang 2009), where the rate for length

`L`

is proportional to`{L * max_length / (max_length - L + 1)}^(-a)`

. This method will be used if the following arguments are provided:`rate`

`max_length`

`a`

Directly specify values by providing a numeric vector of relative rates for each insertion/deletion length from 1 to the maximum length. This method will be used if the following arguments are provided:

`rate`

`rel_rates`

Albers, C. A., G. Lunter, D. G. MacArthur, G. McVean, W. H. Ouwehand, and R. Durbin. 2011. Dindel: accurate indel calls from short-read data. Genome Research 21:961–973.

Fletcher, W., and Z. Yang. 2009. INDELible: a flexible simulator of biological sequence evolution. Molecular Biology and Evolution 26:1879–1888.

# relative rates are proportional to `exp(-L)` for indel # length `L` from 1 to 5: indel_rates1 <- indels(0.1, max_length = 5) # relative rates are proportional to Lavalette distribution # for length from 1 to 10: indel_rates2 <- indels(0.2, max_length = 10, a = 1.1) # relative rates are all the same for lengths from 1 to 100: indel_rates3 <- indels(0.2, rel_rates = rep(1, 100))