siteFrequency: Get site frequency spectrum of a tree

In cloneRate: Estimate Growth Rates from Phylogenetic Trees

Get site frequency spectrum of a tree

Description

siteFrequency() calculates the site frequency in units of time or mutations, as well as a normalized frequency.

Usage

siteFrequency(tree, includeStem = FALSE)

Arguments

tree	An ultrametric or mutation-based tree subset to include only the clone of interest. Alternatively, a list with several such trees.
includeStem	Boolean indicating whether we should count the stem of the tree as contributing to the site frequency distribution. Default is FALSE.

Value

A data.frame with three columns: the number of descendant cells, site frequency in units of time or mutations, and normalized site frequency. If a list of trees is input, output will be a list of such data.frames.

See Also

internalLengths() and sharedMuts() which use the sum of edge lengths ancestral to between 2 and n-1 tips to calculate a growth rate.

Examples

# Get site frequency of a single tree
example.df <- siteFrequency(exampleUltraTrees[[1]])

# Get site frequency of a list of trees
example.list <- siteFrequency(exampleMutTrees)

cloneRate documentation built on Sept. 22, 2023, 5:09 p.m.