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.

Install the latest version of this package by entering the following in R:
install.packages("starmie")
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

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