findSites {sitePath}R Documentation

Finding sites with variation

Description

Single nucleotide polymorphism (SNP) in the whole package refers to variation of amino acid. findSNPsite will try to find SNP in the multiple sequence alignment. A reference sequence and gap character may be specified to number the site. This is irrelevant to the intended analysis but might be helpful to evaluate the performance of fixationSites.

After finding the lineagePath of a phylogenetic tree, fixationSites uses the result to find those sites that show fixation on some, if not all, of the lineages. Parallel evolution is relatively common in RNA virus. There is chance that some site be fixed in one lineage but does not show fixation because of different sequence context.

After finding the lineagePath of a phylogenetic tree, multiFixationSites uses random sampling on the original tree and applies the method used in fixationSites to each sampled tree and summarize the results from all the samples.

Usage

SNPsites(tree, minSNP = NULL)

## S3 method for class 'lineagePath'
fixationSites(
  paths,
  minEffectiveSize = NULL,
  searchDepth = 1,
  method = c("compare", "insert", "delete"),
  ...
)

## S3 method for class 'lineagePath'
multiFixationSites(
  paths,
  samplingSize = NULL,
  samplingTimes = 100,
  minEffectiveSize = 0,
  searchDepth = 1,
  method = c("compare", "insert", "delete"),
  ...
)

Arguments

tree

The return from addMSA function

minSNP

Minimum number of amino acid variation to be a SNP

paths

a lineagePath object returned from lineagePath function or a phylo object after addMSA

minEffectiveSize

A vector of two integers to specifiy minimum tree tips involved before/after mutation. Otherwise the mutation will not be counted into the return. If more than one number is given, the ancestral takes the first and descendant takes the second as the minimum. If only given one number, it's the minimum for both ancestral and descendant.

searchDepth

The function uses heuristic search but the termination of the search cannot be intrinsically decided. searchDepth is needed to tell the search when to stop.

method

The strategy for predicting the fixation. The basic approach is entropy minimization and can be achieved by adding or removing fixation point, or by comparing the two.

...

further arguments passed to or from other methods.

samplingSize

The number of tips sampled for each round of resampling. It shoud be at least 10th and at most nine 10ths of the tree tips.

samplingTimes

The total times of random sampling to do. It should be greater than 100.

Value

SNPsite returns a list of qualified SNP site

fixationSites returns a list of fixation mutations with names of the tips involved.

multiFixationSites returns sites with multiple fixations.

Examples

data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
SNPsites(tree)
fixationSites(lineagePath(tree))

[Package sitePath version 1.4.2 Index]