Package: metabomxtr 1.41.0

Michael Nodzenski

metabomxtr: A package to run mixture models for truncated metabolomics data with normal or lognormal distributions

The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.

Authors:Michael Nodzenski, Anna Reisetter, Denise Scholtens

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NEWS

# Install 'metabomxtr' in R:

install.packages('metabomxtr', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

euMetabCData - A sample data set of truncated metabolomics data.
euMetabData - A sample data set of truncated metabolomics data.
metabdata - A sample data set of truncated metabolomics data

On BioConductor:metabomxtr-1.41.0(bioc 3.21)metabomxtr-1.40.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology metabolomics massspectrometry

3.60 score 5 scripts 250 downloads 17 exports 49 dependencies

Last updated 2 months agofrom:26b046c429. Checks:OK: 7. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 29 2024
R-4.5-win	OK	Dec 29 2024
R-4.5-linux	OK	Dec 29 2024
R-4.4-win	OK	Dec 29 2024
R-4.4-mac	OK	Dec 29 2024
R-4.3-win	OK	Dec 29 2024
R-4.3-mac	OK	Dec 29 2024

Exports:addBatchMeans addOutlierInfo allMissingLevels anyMissingLevels idMissingLevels metabplot mixnorm mxtrmod mxtrmodLL mxtrmodLRT mxtrmodstart removeAllMissingCatVar removeMissingLevels runMxtrmod xdesign yvals zdesign

Dependencies:BH Biobase BiocGenerics BiocParallel cli codetools colorspace cpp11 fansi farver formatR Formula futile.logger futile.options generics ggplot2 glue gtable isoband labeling lambda.r lattice lifecycle magrittr MASS Matrix mgcv multtest munsell nlme nloptr numDeriv optimx pillar pkgconfig plyr pracma R6 RColorBrewer Rcpp rlang scales snow survival tibble utf8 vctrs viridisLite withr

metabomxtr

Rendered fromMetabomxtr_Vignette.Rnwusingutils::Sweaveon Dec 29 2024.

Last update: 2022-08-17
Started: 2015-04-20

mixnorm

Rendered frommixnorm_Vignette.Rnwusingutils::Sweaveon Dec 29 2024.

Last update: 2022-08-17
Started: 2015-09-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A package to run mixture models on truncated normal or lognormal data	metabomxtr-package metabomxtr
A function to append batch specific mean metabolite abundances to data frames containing raw values.	addBatchMeans
A function to determine whether specific metabolite observations are outliers.	addOutlierInfo
A function to determine whether metabolite levels are present for at most one level of a categorical variable.	allMissingLevels
A function to determine whether any level of a categorical variable has completely missing outcome (metabolite) data	anyMissingLevels
A sample data set of truncated metabolomics data.	euMetabCData
A sample data set of truncated metabolomics data.	euMetabData
A function to determine the levels of a categorical variable with completely missing outcome data.	idMissingLevels
A sample data set of truncated metabolomics data	metabdata
A function to plot metabolite abundance before and after normalization.	metabplot
A function to perform per-metabolite batch normalization using a mixture model with batch-specific thresholds and run order correction if desired.	mixnorm
A function to return optimized parameter estimates and the negative log-likelihood of mixture models for truncated normal or lognormal data	mxtrmod
A function to return the negative log-likelihood of mixture models of truncated, normal or lognormal data	mxtrmodLL
A function to run likelihood ratio tests on full vs. reduced mixture models	mxtrmodLRT
A function to generate starting parameter estimates for the optimization of mixture model parameters	mxtrmodstart
A function to remove categorical variables with insufficient data to estimate effects from mixture models	removeAllMissingCatVar
A function to remove levels of categorical variables with completely missing outcome data from data frames or matrices.	removeMissingLevels
A function to return optimized parameter estimates and the negative log-likelihood of mixture models for truncated normal or lognormal data	runMxtrmod
~~ Methods for Function 'xdesign' ~~	xdesign xdesign,data.frame-method xdesign,ExpressionSet-method xdesign,matrix-method xdesign-methods
~~ Methods for Function 'yvals' ~~	yvals yvals,data.frame,character-method yvals,ExpressionSet,character-method yvals,matrix,character-method yvals-methods
~~ Methods for Function 'zdesign' ~~	zdesign zdesign,data.frame-method zdesign,ExpressionSet-method zdesign,matrix-method zdesign-methods