Description Usage Arguments Details Value References Examples
Construct necessary information for insertions and deletions (indels) that will
be used in create_variants
.
1 
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 
All indels require the rate
parameter, which specifies
the overall indels rate among all lengths.
The rate
parameter is ultimately combined with a vector of relative rates among
the different lengths of indels from 1 to the maximum possible length.
There are three different ways to specify/generate relativerate 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
An indel_info
object, which is an R6 class that wraps the info needed for
the create_variants
function.
It does not allow the user to directly manipulate the info inside, as that
should be done using this function.
You can use the rates()
method to view the indel rates by size.
Albers, C. A., G. Lunter, D. G. MacArthur, G. McVean, W. H. Ouwehand, and R. Durbin. 2011. Dindel: accurate indel calls from shortread 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.
1 2 3 4 5 6 7 8 9 10  # 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))

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