buildLocalTrees: Build a tree for each window

Description Usage Arguments Details Value

View source: R/buildSubTrees.R

Description

Build local trees for each window along a contig.

Usage

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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 March 19, 2018, 4:07 a.m.