paraFixSites: The fixation sites with mutation on parallel lineage

Description Usage Arguments Value Examples

View source: R/paraFixSites.R

Description

The operation between the results of fixationSites and parallelSites.

Usage

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paraFixSites(x, ...)

## S3 method for class 'lineagePath'
paraFixSites(
  x,
  category = c("intersect", "union", "parallelOnly", "fixationOnly"),
  minEffectiveSize = NULL,
  searchDepth = 1,
  method = c("compare", "insert", "delete"),
  minSNP = NULL,
  mutMode = c("all", "exact", "pre", "post"),
  ...
)

## S3 method for class 'sitesMinEntropy'
paraFixSites(
  x,
  category = c("intersect", "union", "parallelOnly", "fixationOnly"),
  minSNP = NULL,
  mutMode = c("all", "exact", "pre", "post"),
  ...
)

Arguments

x

A lineagePath object returned from lineagePath function.

...

further arguments passed to or from other methods.

category

Could be parallelOnly, fixationOnly, intersect or union.

minEffectiveSize

The minimum number of tips in a group.

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.

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 paraFixSites object.

Examples

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