globalDeletion: globalDeletion

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

Description

This function returns a DNAStringSet reduced by all sites containing any gaps ("-", "+", ".") or missing ("N") sites.

Usage

globalDeletion(dna, x.pos = NULL, wlen = 50000, start.by = 1,
  end.by = NULL, threads = 1, pB = FALSE)

Arguments

dna	DNAStringSet
x.pos	population X positions [default: NULL]
wlen	sliding window length [default: 50000]
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

pairwiseDeletion, biSites, triSites

Examples

data("MySequences", package="distIUPAC")
mySubSequence<-globalDeletion(MySequences)

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