dist.xyStats: dist.xyStats

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).

Usage

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

Arguments

tmpSEQ	DNAStringSet [mandatory]
x.pos	population X positions [mandatory]
y.pos	population Y positions [mandatory]
x.name	population X name [default: "x"]
y.name	population Y name [default: "y"]
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]

Author(s)

Kristian K Ullrich

References

Slatkin, M. (1991). Inbreeding coefficients and coalescence times. Genetics Research, 58(2), 167-175.

Beerli, P. (1998). Structured Populations. Advances in molecular ecology, 306, 39.

Reich, D., Thangaraj, K., Patterson, N., Price, A. L., & Singh, L. (2009). Reconstructing Indian population history. Nature, 461(7263), 489.

Patterson, N., Moorjani, P., Luo, Y., Mallick, S., Rohland, N., Zhan, Y., ... & Reich, D. (2012). Ancient admixture in human history. Genetics, 192(3), 1065-1093.

Peter, B. M. (2016). Admixture, population structure, and F-statistics. Genetics, 202(4), 1485-1501.

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

xyStats, distIUPAC, rcpp_distIUPAC, dist.dna

Examples

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

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

##Here, one needs to consider the changed x and y 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)))

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

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

##compare results
rbind(CAS_AFG.pairwiseDeletion.xyStats, CAS_AFG.globalDeletion.xyStats)

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