dist.xStats: dist.xStats

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).

Usage

dist.xStats(tmpSEQ, x.pos = NULL, x.name = "x", dist = "IUPAC",
  ncores = 1)

Arguments

tmpSEQ	DNAStringSet [mandatory]
x.pos	population X positions [default: NULL]
x.name	population X name [default: "x"]
dist	distance to use, choose one model as in dist.dna or [default: "IUPAC"]
ncores	number of parallel cores to process pairwise distance calculation [default: 1] see rcpp_distIUPAC [default: 1]

Author(s)

Kristian K Ullrich

References

Paradis, E., & Schliep, K. (2018). ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526-528.

See Also

xStats, distIUPAC, rcpp_distIUPAC, dist.dna

Examples

##Use the 'xStats' function to handle population assignment automatically

##load sequence data
data("MySequences", package="distIUPAC")
CAS.pos<-5:34

##pairwise deletion
CAS.pairwiseDeletion.dist<-distIUPAC(as.character(MySequences[CAS.pos]))
CAS.pairwiseDeletion.xStats<-dist.xStats(
  CAS.pairwiseDeletion.dist, x.name="CAS")

##global deletion
CAS.globalDeletion.dist<-distIUPAC(
  as.character(globalDeletion(MySequences[CAS.pos])))
CAS.globalDeletion.xStats<-dist.xStats(
  CAS.globalDeletion.dist, x.name="CAS")

##compare results
rbind(CAS.pairwiseDeletion.xStats, CAS.globalDeletion.xStats)

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