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Growth rate estimate using the sum of shared mutations assuming a mutation tree

Source: R/growthRateMethods.R
sharedMuts.Rd

sharedMuts() provides an estimate for the net growth rate of the clone with confidence bounds, using the shared mutations method.

Usage

sharedMuts(tree, nu = NULL, alpha = 0.05, allow.ultrametric = F)

Arguments

tree

A non-ultrametric ape tree subset to include only the clone of interest

nu

The mutation rate. If none given, sharedMuts() will first look for a nu column in a metadata data.frame of the tree, and then look for a nu in the tree itself. Will throw error if no nu given or found.

alpha

Used for calculation of confidence intervals. 1-alpha confidence intervals used with default of alpha = 0.05 (95 percent confidence intervals)

allow.ultrametric

Bool. By default, returns an error for ultrametric tree, but can override by setting this to TRUE.

Value

A dataframe including the net growth rate estimate, the sum of internal lengths and other important details (clone age estimate, runtime, n, etc.)

See also

internalLengths() which is the ultrametric/time-based analogue

Examples

sharedMuts(cloneRate::exampleMutTrees[[1]])
#>   lowerBound estimate upperBound       nu cloneAgeEstimate sharedMutations
#> 1  0.7208325 0.907424   1.094015 18.46608         20.32646            2035
#>   privateMutations extIntRatio   n alpha runtime_s     method
#> 1            24393    11.98673 100  0.05     0.005 sharedMuts