fixationPath: Accumulation of fixed mutation as a tree

Description Usage Arguments Value Examples

View source: R/fixationPath.R

Description

The tips are clustered according to the fixation sites. The transition of fixation sites will be plotted as a phylogenetic tree. The length of each branch represents the number of fixation mutation between two clusters. The name of the tree tips indicate the number of sequences in the cluster.

Usage

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fixationPath(x, ...)

## S3 method for class 'sitesMinEntropy'
fixationPath(x, minEffectiveSize = NULL, ...)

## S3 method for class 'fixationSites'
fixationPath(x, minEffectiveSize = NULL, ...)

Arguments

x

The return from fixationSites function.

...

Further arguments passed to or from other methods.

minEffectiveSize

The minimum size for a tip cluster.

Value

An fixationPath object

Examples

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data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
paths <- lineagePath(tree)
mutations <- fixationSites(paths)
fixationPath(mutations)

wuaipinglab/sitePath documentation built on July 25, 2021, 9:11 p.m.