dist.xyiStats: dist.xyiStats

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

Description

This function calculates distIUPAC based distances comparing two populations (x: receiver; y: donor) with an ingroup population (i: ingroup). In a four-taxin scenario (((P1,P2),P3),O) with geneflow from P3>>P2, the populations should be defined for deltaMean and deltaMin statistics as follows [x:P2 y:P3 i:P1]. Accordingly in the four-taxin scenario (((P1,P2),P3),O) with geneflow from P2>>P3, the populations should be defined for deltaMean and deltaMin statistics as follows [x:P3 y:P2 i:P1].

Usage

dist.xyiStats(tmpSEQ, x.pos, y.pos, i.pos, x.name = "x", y.name = "y",
  i.name = "i", dist = "IUPAC", ncores = 1)

Arguments

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

Author(s)

Kristian K Ullrich

See Also

xyiStats, distIUPAC, rcpp_distIUPAC

Examples

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

##load sequence data
data("MySequences", package="distIUPAC")
CAS.pos<-5:34
AFG.pos<-82:87
IRA.pos<-71:78

##Here, one needs to consider the changed x, y and i positions due
##to sub-sampling.
CAS.pos_<-seq_along(CAS.pos)
AFG.pos_<-seq(from=length(CAS.pos_)+1, to=length(c(CAS.pos, AFG.pos)))
IRA.pos_<-seq(from=length(c(CAS.pos, AFG.pos))+1,
to=length(c(CAS.pos, AFG.pos, IRA.pos)))

##pairwise deletion
CAS_AFG_IRA.pairwiseDeletion.dist<-distIUPAC(
  as.character(MySequences[c(CAS.pos,AFG.pos,IRA.pos)]))
CAS_AFG_IRA.pairwiseDeletion.xyiStats<-dist.xyiStats(
  CAS_AFG_IRA.pairwiseDeletion.dist, 
  x.pos=CAS.pos_, y.pos=AFG.pos_, i.pos=IRA.pos_,
  x.name="CAS", y.name="AFG", i.name="IRA")

##global deletion
CAS_AFG_IRA.globalDeletion.dist<-distIUPAC(
  as.character(globalDeletion(MySequences[c(CAS.pos,AFG.pos,IRA.pos)])))
CAS_AFG_IRA.globalDeletion.xyiStats<-dist.xyiStats(
  CAS_AFG_IRA.globalDeletion.dist,
  x.pos=CAS.pos_, y.pos=AFG.pos_, i.pos=IRA.pos_,
  x.name="CAS", y.name="AFG", i.name="IRA")

##compare results
rbind(CAS_AFG_IRA.pairwiseDeletion.xyiStats,
  CAS_AFG_IRA.globalDeletion.xyiStats)

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