metaMix: Bayesian Mixture Analysis for Metagenomic Community Profiling

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Resolves complex metagenomic mixtures by analysing deep sequencing data, using a mixture model based approach. The use of parallel Monte Carlo Markov chains for the exploration of the species space enables the identification of the set of species more likely to contribute to the mixture.

Author
Sofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
Date of publication
2015-03-15 14:03:01
Maintainer
Sofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
License
GPL-3
Version
0.2

View on CRAN

Man pages

bayes.model.aver
Bayesian Model Averaging
generative.prob
Compute generative probabilities from BLAST output
parallel.temper
Parallel Tempering MCMC
parallel.temper.nucl
Parallel Tempering MCMC
reduce.space
Reduce the space of potential species by fitting the mixture...
step1
Example output of generative.prob() for use in the...
step2
Example output of reduce.space() for use in the...
step3
Example output of parallel.temper() for use in the...

Files in this package

metaMix
metaMix/inst
metaMix/inst/extdata
metaMix/inst/extdata/PT_plots.RData
metaMix/inst/extdata/gi_taxid_prot_example.dmp
metaMix/inst/extdata/blastOut_custom.tab
metaMix/inst/extdata/read_lengths.tab
metaMix/inst/extdata/read_weights.tab
metaMix/inst/extdata/blastOut_default.tab
metaMix/inst/extdata/dat1
metaMix/inst/extdata/dat1/step4.RData
metaMix/inst/extdata/dat1/step2.RData
metaMix/inst/extdata/dat1/gi_taxid_prot_example.dmp
metaMix/inst/extdata/dat1/step3.RData
metaMix/inst/extdata/dat1/blastOut2.tab
metaMix/inst/extdata/dat1/read_lengths.tab
metaMix/inst/extdata/dat1/removeID.tab
metaMix/inst/extdata/dat1/read_weights.tab
metaMix/inst/extdata/dat1/blastOut_old.tab
metaMix/inst/extdata/dat1/remove.sh
metaMix/inst/extdata/dat1/blastOut.tab
metaMix/inst/extdata/dat1/names_example.dmp.bck
metaMix/inst/extdata/dat1/names_example.dmp
metaMix/inst/extdata/names_example.dmp
metaMix/inst/doc
metaMix/inst/doc/guide.Rnw
metaMix/inst/doc/guide.R
metaMix/inst/doc/guide.pdf
metaMix/src
metaMix/src/fast_multinom_weight.cpp
metaMix/NAMESPACE
metaMix/data
metaMix/data/step2.RData
metaMix/data/step3.RData
metaMix/data/step1.RData
metaMix/R
metaMix/R/step3_parallelTemper_nucl.R
metaMix/R/Gibbs.R
metaMix/R/step2_allInclusive_MM.R
metaMix/R/step1_preprocess.R
metaMix/R/getArgs.R
metaMix/R/step4_bayesModelAver.R
metaMix/R/metaMix-package.r
metaMix/R/EM.R
metaMix/R/logmean.R
metaMix/R/computePenalty.R
metaMix/R/step3_parallelTemper.R
metaMix/R/zzz.R
metaMix/vignettes
metaMix/vignettes/guide.Rnw
metaMix/vignettes/guide.Rnw.bck
metaMix/MD5
metaMix/build
metaMix/build/vignette.rds
metaMix/DESCRIPTION
metaMix/man
metaMix/man/bayes.model.aver.Rd
metaMix/man/step2.Rd
metaMix/man/step3.Rd
metaMix/man/generative.prob.Rd
metaMix/man/parallel.temper.Rd
metaMix/man/parallel.temper.nucl.Rd
metaMix/man/reduce.space.Rd
metaMix/man/step1.Rd