Description Usage Arguments Author(s) See Also Examples
This function returns tri-allelic site positions given
a dna object DNAStringSet
, also with IUPAC code.
1 2 |
dna |
|
x.pos |
population X positions [default: NULL] |
min.ind |
minimum number of individuals without gaps ("-", "+", ".") or without missing sites ("N"), set to size of population ("length(x.pos)") to mask global deletion sites [default: 0] |
wlen |
sliding window length [default: 25000] |
start.by |
optional start position[default: 1] |
end.by |
optional end position [default: NULL] |
threads |
number of parallel threads [default: 1] |
pB |
specifies if progress should be shown as a progress bar [default: FALSE] |
Kristian K Ullrich
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | ##load sequence data
data("MySequences", package="distIUPAC")
##consider all sequences
MySequences.triSites<-triSites(MySequences)
as.matrix(MySequences)[,head(MySequences.triSites$triPOS)]
##consider only a subset of all sequences
CAS.pos<-5:34
CAS.triSites<-triSites(MySequences, x.pos=CAS.pos)
as.matrix(MySequences[CAS.pos])[, head(CAS.triSites$triPOS)]
##consider only sites were 15 individuals have no gaps or missing sites
CAS.triSites.minInd.15<-triSites(MySequences, x.pos=CAS.pos, min.ind=15)
as.matrix(MySequences[CAS.pos])[, head(CAS.triSites.minInd.15$triPOS)]
as.matrix(MySequences[CAS.pos])[, head(CAS.triSites.minInd.15$triPOSmasked)]
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