dmngroup {DirichletMultinomial} | R Documentation |
Fit Dirichlet-Multinomial generative classifiers to groups (rows) within a sample x taxon count matrix.
dmngroup(count, group, k, ..., simplify = TRUE, .lapply = parallel::mclapply)
count |
|
group |
|
k |
|
... |
Additional arguments, passed to |
simplify |
Return only the best-fit model for each group? |
.lapply |
An |
This function divided count
into groups defined by
group
, creates all combinations of group
x k
,
and evaluates each using dmn
. When simplify=TRUE
,
the best (Laplace) fit is selected for each group.
An object of class dmngroup
, a list of fitted models of class
dmn
. When simplify=TRUE
, elements are named by
the group to which they correspond.
Martin Morgan mailto:mtmorgan@fhcrc.org
Holmes I, Harris K, Quince C, 2012 Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics. PLoS ONE 7(2): e30126. doi:10.1371/journal.pone.0030126.
dmn
, DirichletMultinomial-package,
vignette("DirichletMultinomial")
## best fit for groups 'Lean' and 'Obese'; full example in vignette. ## Not run: bestgrp <- dmngroup(count, pheno, k=1:5, verbose=TRUE, mc.preschedule=FALSE) ## End(Not run) data(bestgrp) bestgrp bestgrp[["Obese"]]