Description Usage Arguments Author(s) References See Also Examples
This function calculates distIUPAC
based distances
comparing all possible pairwise population combinations (x: receiver and
y: donor).
1 2 3 4 | xyMultiStats(dna, pop.list, 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 = TRUE)
|
dna |
|
pop.list |
population list with individual positions [mandatory] |
chr.name |
chromosome name [default: "chr"] |
wlen |
sliding windows length [default: 25000] |
wjump |
sliding windows jump [default: 25000] |
start.by |
optional start position [deafult: 1] |
end.by |
optional end position [deafult: NULL] |
wtype |
sliding windows type to use |
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: TRUE] |
Kristian K Ullrich
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 | ##load sequence data
data("MySequences", package="distIUPAC")
CAS.pos<-5:34
AFG.pos<-82:87
SPRE.pos<-106:113
pop.list<-setNames(list(CAS.pos, AFG.pos, SPRE.pos), c("CAS", "AFG",
"SPRE"))
##sliding windows based on base-pair length
CAS.AFG.SPRE.xyMultiStats<-xyMultiStats(MySequences, pop.list=pop.list,
threads = 2)
CAS.AFG.SPRE.xyMultiStats
#sliding windows based on biSites
CAS.AFG.SPRE.xyMultiStats<-xyMultiStats(MySequences, list.pos = pop.list,
wtype = "biSites", wlen = 50, threads = 2)
CAS.AFG.SPRE.xyMultiStats
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