iupac2gphocs: iupac2gphocs

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

Description

This function returns loci blocks as G-PhoCS-like output.

Usage

iupac2gphocs(dna, chr = "1", wlen = 25000, start.by = NULL,
  end.by = NULL, threads = 1, pB = TRUE)

Arguments

dna	DNAStringSet
chr	set chromosome name
wlen	sliding window length for loci 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")
gphocs<-iupac2gphocs(MySequences, threads = 2)
str(gphocs)
#sink("seqs-sample.txt")
#cat(gphocs,sep="\n")
#sink(NULL)

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