bam2consensus: bam2consensus

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

bam2consensus(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 = TRUE)

Arguments

chr.name	chromosome name [default: NULL]
wlen	sliding windows length [default: 100000]
wjump	sliding windows jump [default: 100000]
start.by	optional start position [default: NULL]
end.by	optional end position [default: NULL]
wtype	sliding windows type to use bp, biSites or triSites [default: "bp"] see biSites and triSites
dist	distance to use
global.deletion	a logical indicating whether to delete the sites with missing data in a global [TRUE] or pairwise way [FALSE]
threads	number of parallel threads to process sliding windows
ncores	number of parallel cores to process pairwise distance calculation [default: 1] see rcpp_distIUPAC
pB	specifies if progress should be shown as a progress bar
pop.list	population list
pop.names	population names [default: NULL]

Author(s)

Kristian K Ullrich

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.