iupac2pomo: iupac2pomo

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

Description

This function returns sites as IQ-TREE PoMo-like output.

Usage

iupac2pomo(dna, list.pos, chr = "1", wlen = 25000, start.by = NULL,
  end.by = NULL, threads = 1, pB = TRUE)

Arguments

dna	DNAStringSet
list.pos	population positions list
chr	set chromosome name
wlen	sliding window length for PoMo sites 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.pomo<-iupac2pomo(MySequences, list.pos = pop.list, threads = 2)
head(CAS.AFG.SPRE.pomo)

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