clumpp: Run CLUMPP

In EricArcher/strataG: Summaries and Population Structure Analyses of Genetic Data

Run CLUMPP

Description

Run CLUMPP to aggregate multiple STRUCTURE runs.

Usage

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 [e-mail]

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

EricArcher/strataG documentation built on Feb. 12, 2023, 4:11 a.m.