xyStats: 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 and y: donor).

Usage

xyStats(dna, x.pos, y.pos, x.name = "x", y.name = "y",
  chr.name = "chr", wlen = 25000, wjump = 25000, start.by = 1,
  end.by = NULL, wtype = "bp", dist = "IUPAC",
  global.deletion = TRUE, threads = 1, ncores = 1, pB = FALSE)

Arguments

dna	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"]
chr.name	chromosome name [default: "chr"]
wlen	sliding windows length [default: 25000]
wjump	sliding windows jump [default: 25000]
start.by	optional start position [default: 1]
end.by	optional end position [default: NULL]
wtype	sliding windows type to use bp, biSites or triSites [default: "bp"]
dist	distance to use, choose one model as in dist.dna or [default: "IUPAC"]
global.deletion	a logical indicating whether to delete the sites with missing data in a global or pairwise way (default is to delete in a global way) [default: TRUE]
threads	number of parallel threads [default: 1]
ncores	number of parallel cores to process pairwise distance calculation [default: 1]
pB	specifies if progress should be shown as a progress bar [default: FALSE]

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

dist.xyStats, dist.dna

Examples

##load sequence data
data("MySequences", package="distIUPAC")
CAS.pos<-5:34
AFG.pos<-82:87
##sliding windows based on base-pair length
CAS.AFG.xyStats<-xyStats(MySequences, x.pos=CAS.pos, y.pos=AFG.pos,
x.name="CAS", y.name="AFG", threads=2)
CAS.AFG.xyStats
##sliding windows based on biSites
CAS.AFG.xyStats<-xyStats(MySequences, x.pos=CAS.pos, y.pos=AFG.pos,
wlen=50, wtype="biSites", x.name="CAS", y.name="AFG", threads=2)
CAS.AFG.xyStats

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