DEPRECATED. USE clumppExportMatrix(). Takes multiple ADMIXTURE runs and combines several repeats for each K into a single file along with a parameter file. The two output files are organised into folders by K. The CLUMPP executable file can simply be copied to this folder and run to reorder the clusters for each K.
clumppExportAdmixture(files = NULL, prefix = NA, parammode = NA,
paramrep = NA, useexe = FALSE)A character vector of ADMIXTURE cluster run files to be tabulated.
Use choose.files(multi = TRUE) for interactive selection.
A character prefix for folder names. By default, set to 'ADMIXTUREpop'.
A numeric 1, 2 or 3 indicating the algorithm option for CLUMPP paramfile. Calculated automatically by default. Set this value to 3 if CLUMPP runs too long. See details.
A numeric indicating the number of repeats for CLUMPP paramfile. Calculated automatically by default. See details.
A logical indicating if CLUMPP executable must be run automatically based on system OS (experimental).
The combined file and paramfile are written into respective folders named by population.
When multiple repeats are run for each K in ADMIXTURE, the order of clusters may be jumbled for each run. Therefore, when plotting multiple runs within each K, the colours cannot be assigned correctly. The software CLUMPP helps to overcome this issue by reordering the clusters correctly. This function clumppExportAdmixture() takes multiple runs for each K and combines them into a single file and generates a parameter file for easy use with CLUMPP. Further details for CLUMPP can be found here: Jakobsson, M., and Rosenberg, N. A. (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.
The parammode (M) is the type of algorithm used. Option 1 is 'FullSearch' (takes the longest time), option 2 is 'Greedy' and option 3 is 'LargeKGreedy' (fastest). If clumpp takes more than a few minutes, consider changing parammode to a higher number (ex. from 2 to 3), or open the exported paramfile and manually change GREEDY_OPTION to 3.
The parammode and paramrep for CLUMPP paramfile is set based on this calculation. T <- factorial(k)*((runs*(runs-1))/2)*k*ind, where k is number of populations, runs is number of runs for k and ind is number of individuals. If T <= 100000000, then parammode is 2 and paramrep is 20, otherwise parammode is 3 and paramrep is set to 500.
To find out more about parammode (algorithm type) and paramrep (repeats), refer to CLUMPP documentation.
useexe This option automatically runs the CLUMPP executable that is provided with this package. The CLUMPP executable was obtained from https://web.stanford.edu/group/rosenberglab/clumpp.html. Remember to cite CLUMPP if this option is used.