iupac2treemix: iupac2treemix

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

Description

This function returns biallelic sites as treemix-like output.

Usage

iupac2treemix(dna, list.pos, wlen = 25000, start.by = NULL,
  end.by = NULL, threads = 1, pB = TRUE)

Arguments

dna	DNAStringSet
list.pos	population positions list
wlen	sliding window length for biSites retrieval
start.by	optional start position
end.by	optional end position
threads	number of parallel threads
pB	specifies if progress should be shown as a progress bar

Author(s)

Kristian K Ullrich

Examples

data("MySequences", package = "distIUPAC")
CAS.pos<-5:34
AFG.pos<-82:87
SPRE.pos<-106:113
pop.list<-list(CAS.pos, AFG.pos, SPRE.pos)
names(pop.list)<-c("CAS", "AFG", "SPRE")
CAS.AFG.SPRE.treemix<-iupac2treemix(MySequences, list.pos = pop.list, threads = 2)
head(CAS.AFG.SPRE.treemix)

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