metaMix: Bayesian Mixture Analysis for Metagenomic Community Profiling
Version 0.2

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.

Browse man pages Browse package API and functions Browse package files

AuthorSofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
Date of publication2015-03-15 14:03:01
MaintainerSofia Morfopoulou <sofia.morfopoulou.10@ucl.ac.uk>
LicenseGPL-3
Version0.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("metaMix")

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...

Functions

EM Source code
Gibbs Source code
bayes.model.aver Man page Source code
bayes.model.aver.explicit Man page Source code
computePenalty Source code
computePenalty.nucl Source code
generative.prob Man page Source code
generative.prob.nucl Man page Source code
getArgs Source code
logmean Source code
onLoad Source code
parallel.temper Man page Source code
parallel.temper.explicit Man page Source code
parallel.temper.nucl Man page Source code
parallel.temper.nucl.explicit Man page Source code
reduce.space Man page Source code
reduce.space.explicit Man page Source code
step1 Man page
step2 Man page
step3 Man page

Files

inst
inst/extdata
inst/extdata/PT_plots.RData
inst/extdata/gi_taxid_prot_example.dmp
inst/extdata/blastOut_custom.tab
inst/extdata/read_lengths.tab
inst/extdata/read_weights.tab
inst/extdata/blastOut_default.tab
inst/extdata/dat1
inst/extdata/dat1/step4.RData
inst/extdata/dat1/step2.RData
inst/extdata/dat1/gi_taxid_prot_example.dmp
inst/extdata/dat1/step3.RData
inst/extdata/dat1/blastOut2.tab
inst/extdata/dat1/read_lengths.tab
inst/extdata/dat1/removeID.tab
inst/extdata/dat1/read_weights.tab
inst/extdata/dat1/blastOut_old.tab
inst/extdata/dat1/remove.sh
inst/extdata/dat1/blastOut.tab
inst/extdata/dat1/names_example.dmp.bck
inst/extdata/dat1/names_example.dmp
inst/extdata/names_example.dmp
inst/doc
inst/doc/guide.Rnw
inst/doc/guide.R
inst/doc/guide.pdf
src
src/fast_multinom_weight.cpp
NAMESPACE
data
data/step2.RData
data/step3.RData
data/step1.RData
R
R/step3_parallelTemper_nucl.R
R/Gibbs.R
R/step2_allInclusive_MM.R
R/step1_preprocess.R
R/getArgs.R
R/step4_bayesModelAver.R
R/metaMix-package.r
R/EM.R
R/logmean.R
R/computePenalty.R
R/step3_parallelTemper.R
R/zzz.R
vignettes
vignettes/guide.Rnw
vignettes/guide.Rnw.bck
MD5
build
build/vignette.rds
DESCRIPTION
man
man/bayes.model.aver.Rd
man/step2.Rd
man/step3.Rd
man/generative.prob.Rd
man/parallel.temper.Rd
man/parallel.temper.nucl.Rd
man/reduce.space.Rd
man/step1.Rd
metaMix documentation built on May 19, 2017, 7:12 p.m.