buildLocalTrees: Build a tree for each window

In CMWbio/subTreeCheckR: weavR: Windowed Evolutionary Analysis and Visualisation in R.

Description

Build local trees for each window along a contig.

Usage

buildLocalTrees(fileName, DNAwin, contigs, winSize = 1e+05,
  subModel = "raw", minSites, ploidy = 2, nCores = 2, write = NA)

Arguments

fileName	character. Full path name for a Tabix indexed VCF file.
DNAwin	list of multiple DNAbin. A list of already imported VCF files.
contigs	character. Default is "all" Contigs to extract windows from.
winSize	numeric. Default is 100000. Window size in base pairs.
subModel	character. The substitution model to fit to the data. Accepts nucleotide models defined in ape::dist.dna: "raw", "N", "TS", "TV", "JC69", "K80", "F81", "K81", "F84", "BH87", "T92", "TN93", and "GG95."
minSites	numeric. Default is 10 percent of winSize. The minimum number of sites within a window to consider it.
ploidy	numeric. The ploidy of the VCF, as called by Variant Caller.
nCores	numeric. Number of cores to run analysis on.
write	character. Default is NA, will only return the R object. The directory to write the trees out to.

Details

Builds a tree using data from each window across a contig. Defined as a local tree these represent the evolutionary history of the window.

Value

list of trees in phy format. Newick format trees in a specified directory.

CMWbio/subTreeCheckR documentation built on May 26, 2019, 6:41 a.m.