getTrees: getTrees

In kullrich/distIUPAC: calculates IUPAC distances on Biostrings DNAStringSet and BStringSet objects

Description

This function returns nieghbor-joining (njs or bionjs) trees based on distIUPAC based distances rooted to a specific individual.

Usage

getTrees(dna, x.pos = NULL, r.pos = 1, resolve.root = TRUE,
  wlen = 25000, wjump = 25000, start.by = 1, end.by = NULL,
  wtype = "bp", dist = "IUPAC", global.deletion = TRUE,
  model = "bionjs", threads = 1, ncores = 1, x.name = "x",
  r.name = "r", chr.name = "chr", plot = FALSE, pB = FALSE)

Arguments

dna	DNAStringSet
x.pos	population X positions [default: NULL] take all sequences from DNAStringSet
r.pos	root position, needs to be within x.pos [default: 1]
resolve.root	adds a zero-length branch below the MRCA of the ingroup root [default: TRUE]
wlen	sliding windows length [default: 25000]
wjump	sliding windows jump [default: 25000]
start.by	optional start position [default: 1]
end.by	optional end position [default: NULL]
wtype	sliding windows type to use bp, biSites or triSites [default: "bp"]
dist	distance to use, choose one model as in dist.dna or [default: "IUPAC"]
global.deletion	a logical indicating whether to delete the sites with missing data in a global [default: TRUE] or pairwise way [FALSE]
model	tree model to use either njs or bionjs [default: "bionjs"]
threads	number of parallel threads [default: 1]
ncores	number of parallel cores to process pairwise distance calculation [default: 1]
x.name	population X name [default: "x"]
r.name	root name [default: "r"]
chr.name	chromosome name [default: "chr"]
plot	indicates if tree should be plotted [default: FALSE]
pB	specifies if progress should be shown as a progress bar [default: FALSE]

Author(s)

Kristian K Ullrich

Examples

data("MySequences", package = "distIUPAC")
x.pos<-c(1,2,3,4,5,35,63,71,79,82,88,89,97,105,106,114,115,116,117)
r.pos<-116
trees<-getTrees(MySequences, x.pos = x.pos, r.pos = r.pos,
wlen = 10000, wjump = 10000, x.name = "all", r.name = "Rnor", threads = 1)
trees
trees<-getTrees(MySequences, x.pos = x.pos, r.pos = r.pos,
wlen = 10000, wjump = 10000, x.name = "all", r.name = "Rnor",
threads = 2, plot = TRUE)

kullrich/distIUPAC documentation built on Jan. 9, 2020, 2:50 p.m.