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.

Author
Gerry Tonkin-Hill [aut], Stuart Lee [cre, aut]
Date of publication
2016-11-07 08:12:43
Maintainer
Stuart Lee <lee.s@wehi.edu.au>
License
MIT + file LICENSE
Version
0.1.2
URLs

View on CRAN

Man pages

admix
Constructor for admix object
admixList
Contructor for admixList
averagePairWiseSimilarityH
Average Q matrices.
averageQ
Average Q matrices.
bestK
Determine a suitable K value from multiple Structure runs
clumpak
Run the CLUMPP algorithms.
clumpp
Run the CLUMPP algorithms.
exampleAdmixture
Example admixture runs
exampleStructure
Example structure objects
getClusterAlleleFreqMat
Retrieve estimated within-cluster allele frequencies
getCompleteAlleleFreqMat
Retrieve estimated population allele frequencies
getD
Accessor methods for struct objects
getK
Retrieve the assumed number of populations from 'struct' or...
getQ
Retrieve Q matrix from 'struct' or 'admix' objects.
getStephens
Use the Stephen's method to permute sample labels
loadAdmixture
Read Admixture Output
loadStructure
Read Structure Output
plotBar
Generate a barplot of a Structure or Admixture run.
plotMCMC
Plot STRUCTURE MCMC chains
plotMDS
Plot principal coordinates from Q-matrix, struct or admix...
plotMultiK
Generate a barplot for multiple values of K..
plotTreeBar
Generate a barplot of a Structure or Admixture run.
runStructure
Run STRUCTURE in current path
struct
Constructor for struct object
structList
Constructor for a structList object

Files in this package

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