starmie: Population Structure Model Inference and Visualisation

Data structures and methods for manipulating output of genetic population structure clustering algorithms. 'starmie' can parse output from 'STRUCTURE' (see <https://pritchardlab.stanford.edu/structure.html> for details) or 'ADMIXTURE' (see <https://www.genetics.ucla.edu/software/admixture/> for details). 'starmie' performs model selection via information criterion, and provides functions for MCMC diagnostics, correcting label switching and visualisation of admixture coefficients.

AuthorGerry Tonkin-Hill [aut], Stuart Lee [cre, aut]
Date of publication2016-11-07 08:12:43
MaintainerStuart Lee <lee.s@wehi.edu.au>
LicenseMIT + file LICENSE
Version0.1.2
https://github.com/sa-lee/starmie

View on CRAN

Functions

admix Man page
admixList Man page
averagePairWiseSimilarityH Man page
averageQ Man page
bestK Man page
clumpak Man page
clumpp Man page
exampleAdmixture Man page
exampleStructure Man page
getClusterAlleleFreqMat Man page
getCompleteAlleleFreqMat Man page
getD Man page
getFitStats Man page
getK Man page
getMCMC Man page
getPosterior Man page
getQ Man page
getStephens Man page
loadAdmixture Man page
loadStructure Man page
plotBar Man page
plotMCMC Man page
plotMDS Man page
plotMultiK Man page
plotTreeBar Man page
runStructure Man page
struct Man page
structList Man page

Files

starmie
starmie/inst
starmie/inst/vignette-supp
starmie/inst/vignette-supp/plot-bar2-1.png
starmie/inst/vignette-supp/evanno-lyf-1.png
starmie/inst/vignette-supp/clump-example-1.png
starmie/inst/vignette-supp/plotMDS-1.png
starmie/inst/vignette-supp/unnamed-chunk-2-1.png
starmie/inst/vignette-supp/mcmc1-1.png
starmie/inst/vignette-supp/plot-multiK-1.png
starmie/inst/vignette-supp/plot-bar-1.png
starmie/inst/vignette-supp/evanno-lyf-2.png
starmie/inst/extdata
starmie/inst/extdata/hapmap3_files
starmie/inst/extdata/hapmap3_files/hapmap3.1.Q
starmie/inst/extdata/hapmap3_files/hapmap3.5.P
starmie/inst/extdata/hapmap3_files/hapmap3.2.P
starmie/inst/extdata/hapmap3_files/hapmap3.3.P
starmie/inst/extdata/hapmap3_files/hapmap3.5.Q
starmie/inst/extdata/hapmap3_files/log1.out
starmie/inst/extdata/hapmap3_files/hapmap3.1.P
starmie/inst/extdata/hapmap3_files/hapmap3.3.Q
starmie/inst/extdata/hapmap3_files/log4.out
starmie/inst/extdata/hapmap3_files/log3.out
starmie/inst/extdata/hapmap3_files/hapmap3.fam
starmie/inst/extdata/hapmap3_files/log2.out
starmie/inst/extdata/hapmap3_files/hapmap3.4.Q
starmie/inst/extdata/hapmap3_files/log5.out
starmie/inst/extdata/hapmap3_files/hapmap3.4.P
starmie/inst/extdata/hapmap3_files/hapmap3.map
starmie/inst/extdata/hapmap3_files/hapmap3.2.Q
starmie/inst/extdata/microsat_testfiles
starmie/inst/extdata/microsat_testfiles/run2_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run10_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run2_locprior_K5.out_f
starmie/inst/extdata/microsat_testfiles/run9_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/extraparams
starmie/inst/extdata/microsat_testfiles/chain_K6.log
starmie/inst/extdata/microsat_testfiles/run2_locprior_K4.out_f
starmie/inst/extdata/microsat_testfiles/run8_chain_K10.log
starmie/inst/extdata/microsat_testfiles/run8_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run2_locprior_K6.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run7_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run2_locprior_K1.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K4.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K2.out_f
starmie/inst/extdata/microsat_testfiles/run4_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run5_chain_K10.log
starmie/inst/extdata/microsat_testfiles/run6_chain_K10.log
starmie/inst/extdata/microsat_testfiles/run2_locprior_K3.out_f
starmie/inst/extdata/microsat_testfiles/run5_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run2_locprior_K2.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K6.out_f
starmie/inst/extdata/microsat_testfiles/chain_K10.log
starmie/inst/extdata/microsat_testfiles/run4_chain_K10.log
starmie/inst/extdata/microsat_testfiles/locprior_K1.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K9.out_f
starmie/inst/extdata/microsat_testfiles/run2_locprior_K8.out_f
starmie/inst/extdata/microsat_testfiles/run10_chain_K10.log
starmie/inst/extdata/microsat_testfiles/run2_locprior_K7.out_f
starmie/inst/extdata/microsat_testfiles/run3_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K8.out_f
starmie/inst/extdata/microsat_testfiles/mainparams
starmie/inst/extdata/microsat_testfiles/run6_locprior_K10.out_f
starmie/inst/extdata/microsat_testfiles/run2_chain_K10.log
starmie/inst/extdata/microsat_testfiles/run9_chain_K10.log
starmie/inst/extdata/microsat_testfiles/locprior.str
starmie/inst/extdata/microsat_testfiles/run2_locprior_K9.out_f
starmie/inst/extdata/microsat_testfiles/run3_chain_K10.log
starmie/inst/extdata/microsat_testfiles/locprior_K5.out_f
starmie/inst/extdata/microsat_testfiles/locprior_K3.out_f
starmie/inst/extdata/microsat_testfiles/run7_chain_K10.log
starmie/inst/extdata/microsat_testfiles/locprior_K7.out_f
starmie/inst/extdata/microsat_testfiles/run2_chain_K6.log
starmie/inst/doc
starmie/inst/doc/using-starmie-admixture.html
starmie/inst/doc/using-starmie-admixture.R
starmie/inst/doc/using-starmie.html
starmie/inst/doc/using-starmie.R
starmie/inst/doc/using-starmie.Rmd
starmie/inst/doc/using-starmie-admixture.Rmd
starmie/tests
starmie/tests/testthat.R
starmie/tests/testthat
starmie/tests/testthat/test-bestK.R
starmie/tests/testthat/test-loadStructure.R
starmie/tests/testthat/test-plotMCMC.R
starmie/tests/testthat/test-loadAdmixture.R
starmie/NAMESPACE
starmie/R
starmie/R/plotMDS.R starmie/R/plotTreeBar.R starmie/R/bestK.R starmie/R/loadStructure.R starmie/R/averagePairWiseSimilarityH.R starmie/R/plotBar.R starmie/R/clumpp.R starmie/R/admix.R starmie/R/plotMultiK.R starmie/R/clumpak.R starmie/R/loadAdmixture.R starmie/R/run-structure.R starmie/R/get-methods.R starmie/R/plotMCMC.R starmie/R/struct.R starmie/R/averageQ.R
starmie/vignettes
starmie/vignettes/using-starmie.Rmd
starmie/vignettes/using-starmie-admixture.Rmd
starmie/README.md
starmie/MD5
starmie/build
starmie/build/vignette.rds
starmie/DESCRIPTION
starmie/man
starmie/man/loadStructure.Rd starmie/man/admix.Rd starmie/man/runStructure.Rd starmie/man/getClusterAlleleFreqMat.Rd starmie/man/loadAdmixture.Rd starmie/man/bestK.Rd starmie/man/getQ.Rd starmie/man/admixList.Rd starmie/man/plotTreeBar.Rd starmie/man/clumpak.Rd starmie/man/getCompleteAlleleFreqMat.Rd starmie/man/getStephens.Rd starmie/man/plotMDS.Rd starmie/man/getD.Rd starmie/man/plotMultiK.Rd starmie/man/struct.Rd starmie/man/exampleAdmixture.Rd starmie/man/exampleStructure.Rd starmie/man/getK.Rd starmie/man/plotBar.Rd starmie/man/clumpp.Rd starmie/man/averagePairWiseSimilarityH.Rd starmie/man/plotMCMC.Rd starmie/man/averageQ.Rd starmie/man/structList.Rd
starmie/LICENSE

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.