clumpp: Run CLUMPP

Description Usage Arguments Note Author(s) References See Also

View source: R/clumpp.R

Description

Run CLUMPP to aggregate multiple STRUCTURE runs.

Usage

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clumpp(
  sr,
  k,
  align.algorithm = "greedy",
  sim.stat = "g",
  greedy.option = "ran.order",
  repeats = 100,
  order.by.run = 0,
  label = NULL,
  delete.files = TRUE
)

Arguments

sr

result from structure or folder name containing STRUCTURE output files.

k

choice of k in sr to combine.

align.algorithm

algorithm to be used for aligning the runs. Can be "full.search", "greedy", or "large.k".

sim.stat

pairwise matrix similarity statistic to be used. Can be "g" or "g.prime".

greedy.option

input order of runs to be tested. Required if align.algorithm is "greedy" or "large.k". Valid choices are:

all test all possible input orders of runs (note that this option increases the run-time sub-stantially unless R is small).
ran.order test a specified number of random input orders of runs set by the repeats parameter.
repeats

the number of input orders of runs to be tested. Only used if align.algorithm is "greedy" or "large.k", and greedy.option is "ran.order".

order.by.run

permute the clusters according to the cluster order of a specific run. Set this parameter to a number from 1 to the number of runs in sr.

label

label to use for input and output files.

delete.files

logical. Delete all files when CLUMPP is finished?

Note

CLUMPP is not included with strataG and must be downloaded separately. Additionally, it must be installed such that it can be run from the command line in the current working directory. See the vignette for external.programs.

Author(s)

Eric Archer eric.archer@noaa.gov

References

Mattias Jakobsson and Noah A. Rosenberg. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics 23(14):1801-1806. Available at http://web.stanford.edu/group/rosenberglab/clumppDownload.html

See Also

structure


strataG documentation built on Feb. 28, 2020, 9:07 a.m.