parallelSites: Mutation across multiple phylogenetic lineages

In wuaipinglab/sitePath: Phylogeny-based sequence clustering with site polymorphism

Mutation across multiple phylogenetic lineages

Description

A site may have mutated on parallel lineages. Mutation can occur on the same site across the phylogenetic lineages solved by lineagePath. The site will be considered mutated in parallel if the mutation occurs on the non-overlap part of more than two lineages. The amino acid/nucleotide before and after the mutation can be allowed different on different lineages or only the exact same mutations are considered.

Usage

parallelSites(x, ...)

## S3 method for class 'lineagePath'
parallelSites(
  x,
  minSNP = NULL,
  mutMode = c("all", "exact", "pre", "post"),
  ...
)

## S3 method for class 'sitesMinEntropy'
parallelSites(
  x,
  minSNP = NULL,
  mutMode = c("all", "exact", "pre", "post"),
  ...
)

## S3 method for class 'paraFixSites'
parallelSites(x, ...)

Arguments

x	A lineagePath or a sitesMinEntropy object.
...	The arguments in sitesMinEntropy.
minSNP	The minimum number of mutations to be qualified as parallel on at least two lineages. The default is 1.
mutMode	The strategy for finding parallel site. The default all is to consider any mutation regardless of the amino acid/nucleotide before and after mutation; Or exact to force mutation to be the same; Or pre/post to select the site having amino acid/nucleotide before/after mutation.

Value

A parallelSites object

Examples

data(zikv_tree_reduced)
data(zikv_align_reduced)
tree <- addMSA(zikv_tree_reduced, alignment = zikv_align_reduced)
paths <- lineagePath(tree)
x <- sitesMinEntropy(paths)
parallelSites(x)

wuaipinglab/sitePath documentation built on Sept. 26, 2022, 10:16 p.m.