Run STRUCTURE to assess group membership of samples.
structureRun(
g,
k.range = NULL,
num.k.rep = 1,
label = NULL,
delete.files = TRUE,
exec = "structure",
...
)structureWrite(
g,
label = NULL,
maxpops = getNumStrata(g),
burnin = 1000,
numreps = 1000,
noadmix = TRUE,
freqscorr = FALSE,
randomize = TRUE,
seed = 0,
pop.prior = NULL,
locpriorinit = 1,
maxlocprior = 20,
gensback = 2,
migrprior = 0.05,
pfrompopflagonly = TRUE,
popflag = NULL,
...
)
structureRead(file, pops = NULL)
vector of values to for maxpop
in multiple runs.
If set to NULL
, a single STRUCTURE run is conducted with
maxpops
groups. If specified, do not also specify maxpops
.
number of replicates for each value in k.range
.
label to use for input and output files
logical. Delete all files when STRUCTURE is finished?
name of executable for STRUCTURE. Defaults to "structure".
arguments to be passed to structureWrite
.
number of groups.
number of iterations for MCMC burnin.
number of MCMC replicates.
logical. No admixture?
logical. Correlated frequencies?
randomize.
set random seed.
a character specifying which population prior model to use: "locprior" or "usepopinfo".
parameterizes locprior parameter r - how
informative the populations are. Only used when
pop.prior
= "locprior".
specifies range of locprior parameter r. Only used
when pop.prior
= "locprior".
integer defining the number of generations back to test
for immigrant ancestry. Only used when pop.prior
= "usepopinfo".
numeric between 0 and 1 listing migration prior. Only used
when pop.prior
= "usepopinfo".
logical. update allele frequencies from individuals
specified by popflag
. Only used when pop.prior
=
"usepopinfo".
a vector of integers (0, 1) or logicals identifiying whether
or not to use strata information. Only used when pop.prior
= "usepopinfo".
name of the output file from STRUCTURE.
vector of population labels to be used in place of numbers in STRUCTURE file.
structureRun
a list where each element is a list with results
from structureRead
and a vector of the filenames used
structureWrite
a vector of the filenames used by STRUCTURE
structureRead
a list containing:
summary
new locus name, which is a combination of loci in group
q.mat
data.frame of assignment probabilities for each id
prior.anc
list of prior ancestry estimates for each individual where population priors were used
files
vector of input and output files used by STRUCTURE
label
label for the run
Pritchard, J.K., M. Stephens, P. Donnelly. 2000. Inference of population structure using multilocus genotype data. Genetics 155:945-959. http://web.stanford.edu/group/pritchardlab/structure.html
# NOT RUN {
data(msats.g)
# Run STRUCTURE
sr <- structureRun(msats.g, k.range = 1:4, num.k.rep = 10)
# Calculate Evanno metrics
evno <- evanno(sr)
evno
# Run CLUMPP to combine runs for K = 2
q.mat <- clumpp(sr, k = 3)
q.mat
# Plot CLUMPP results
structurePlot(q.mat)
# }
# NOT RUN {
# }
Run the code above in your browser using DataLab