xStats: xStats

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

Description

This function calculates distIUPAC based distances within one population (x: receiver; x: donor) along sliding window.

Usage

xStats(dna, x.pos = NULL, x.name = "x", chr.name = "chr",
  wlen = 25000, wjump = 25000, start.by = 1, end.by = NULL,
  wtype = "bp", dist = "IUPAC", global.deletion = TRUE,
  threads = 1, ncores = 1, pB = FALSE)

Arguments

dna	DNAStringSet
x.pos	population X positions [default: NULL] take all sequences from DNAStringSet
x.name	population X name [default: "x"]
chr.name	chromosome name [default: "chr"]
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 [default: IUPAC] or choose one model as in dist.dna [default: "IUPAC"]
global.deletion	a logical indicating whether to delete the sites with missing data in a global [default: TRUE] or pairwise way [FALSE]
threads	number of parallel threads [default: 1]
ncores	number of parallel cores to process pairwise distance calculation [default: 1]
pB	specifies if progress should be shown as a progress bar [default: FALSE]

Author(s)

Kristian K Ullrich

References

Paradis, E., & Schliep, K. (2018). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526-528.

See Also

dist.xStats, dist.dna

Examples

data("MySequences", package = "distIUPAC")
CAS.pos<-5:34
##multiple threads to process 
CAS.xStats<-xStats(MySequences, x.pos=CAS.pos, x.name="CAS", threads=2)
CAS.xStats

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