dataobjects: Data objects used for examples and the vignette

In DirichletMultinomial: Dirichlet-Multinomial Mixture Model Machine Learning for Microbiome Data

Description

These data objects correspond to steps in a typical work flow, as described in the vignette to this package. fit corresponds to dmn fits to different values of k. bestgroup is the result of the two-group generative classifier. xval summarizes leave-one-out cross validation of the classifier.

Usage

data(fit)
data(bestgrp)
data(xval)

Format

fit is a list of seven DMN objects.

bestgrp is a DMNGroup object.

xval is a data.frame with columns corresponding to the cross-validation group membership and the Lean and Obese posterior probabilities.

Examples

data(fit); fit[1:2]
plot(sapply(fit, laplace), type="b")
data(bestgrp); bestgrp
data(xval); head(xval, 3)

Example output

Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min


Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
[[1]]
class: DMN 
k: 1 
samples x taxa: 278 x 130 
Laplace: 39227.36 BIC: 39527.91 AIC: 39292.11 

[[2]]
class: DMN 
k: 2 
samples x taxa: 278 x 130 
Laplace: 38872.68 BIC: 39588.93 AIC: 39115.53 

class: DMNGroup 
summary:
      k samples taxa       NLE   LogDet   Laplace       BIC       AIC
Lean  1      61  130  9065.657 162.3513  9027.371  9332.864  9195.657
Obese 3     193  130 26769.931 407.4130 26613.414 27801.418 27161.931
        group         Lean     Obese
TS119.2     1 0.0001132595 0.9998867
TS5         2 0.0047642534 0.9952357
TS72        3 0.6170744622 0.3829255

DirichletMultinomial documentation built on Nov. 8, 2020, 7 p.m.