biSites: biSites

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

Description

This function returns bi-allelic site positions given a dna object DNAStringSet, also with IUPAC code.

Usage

biSites(dna, x.pos = NULL, min.ind = 0, wlen = 25000, start.by = 1,
  end.by = NULL, threads = 1, pB = FALSE)

Arguments

dna	DNAStringSet [mandatory]
x.pos	population X positions [default: NULL]
min.ind	minimum number of individuals without gaps ("-", "+", ".") or without missing sites ("N"), set to size of population ("length(x.pos)") to mask global deletion sites [default: 0]
wlen	sliding window length [default: 25000]
start.by	optional start position [default: 1]
end.by	optional end position [default: NULL]
threads	number of parallel threads [default: 1]
pB	specifies if progress should be shown as a progress bar [default: FALSE]

Author(s)

Kristian K Ullrich

See Also

triSites, globalDeletion

Examples

##load sequence data
data("MySequences", package="distIUPAC")

##consider all sequences
MySequences.biSites<-biSites(MySequences)
as.matrix(MySequences)[, head(MySequences.biSites$biPOS)]

##consider only a subset of all sequences
CAS.pos<-5:34
CAS.biSites<-biSites(MySequences, x.pos=CAS.pos)
as.matrix(MySequences[CAS.pos])[, head(CAS.biSites$biPOS)]

##consider only sites were 15 individuals have no gaps or missing sites
CAS.biSites.minInd.15<-biSites(MySequences, x.pos=CAS.pos, min.ind=15)
as.matrix(MySequences[CAS.pos])[, head(CAS.biSites.minInd.15$biPOS)]
as.matrix(MySequences[CAS.pos])[, head(CAS.biSites.minInd.15$biPOSmasked)]

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