Package: MiMIR 1.4

MiMIR: Metabolomics-Based Models for Imputing Risk

Provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.

Authors:Daniele Bizzarri [aut, cre], Marcel Reinders [aut, ths], Marian Beekman [aut], Pieternella Eline Slagboom [aut, ths], Erik van den Akker [aut, ths]

MiMIR_1.4.tar.gz
MiMIR_1.4.zip(r-4.5)MiMIR_1.4.zip(r-4.4)MiMIR_1.4.zip(r-4.3)
MiMIR_1.4.tgz(r-4.4-any)MiMIR_1.4.tgz(r-4.3-any)
MiMIR_1.4.tar.gz(r-4.5-noble)MiMIR_1.4.tar.gz(r-4.4-noble)
MiMIR_1.4.tgz(r-4.4-emscripten)MiMIR_1.4.tgz(r-4.3-emscripten)
MiMIR.pdf |MiMIR.html✨
MiMIR/json (API)
NEWS

# Install 'MiMIR' in R:

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

Bug tracker:https://github.com/danielebizzarri/mimir/issues

Datasets:

Ahola_Olli_betas - T2D-score Betas
BBMRI_hist - BBMRI_hist
BBMRI_hist_scaled - BBMRI_hist_scaled
CVD_score_betas - CVD-score betas
PARAM_metaboAge - PARAMETERS MetaboAge
PARAM_surrogates - PARAMETERS surrogates
acc_LOBOV - Acc_LOBOV
c21 - C21
covid_betas - COVID-score betas
metabo_names_translator - Metabolomics feature nomenclatures
metabolites_subsets - Metabolomics feature subsets
mort_betas - Mortality score betas
phenotypes_names - Phenotypic features names
synthetic_metabolic_dataset - Synthetic metabolomics dataset
synthetic_phenotypic_dataset - Synthetic metabolomics dataset

On CRAN:

binary-risk-factors biomarkers linear-regression metabolites metabolomics nightingale-metabolomics risk-factor-models risk-factors surrogate-models

61 exports 7 stars 1.26 score 180 dependencies 33 scripts 254 downloads

Last updated 2 years agofrom:1746f2d98d. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 18 2024
R-4.5-win	NOTE	Sep 18 2024
R-4.5-linux	NOTE	Sep 18 2024
R-4.4-win	NOTE	Sep 18 2024
R-4.4-mac	NOTE	Sep 18 2024
R-4.3-win	OK	Sep 18 2024
R-4.3-mac	OK	Sep 18 2024

Exports:activateButtn apply.fit apply.fit_surro apply.scale BBMRI_hist_plot binarize_all_pheno BMI_LDL_eGFR calculate_surrogate_scores calib_data_frame calibration_surro comp_covid_score comp.CVD_score comp.mort_score comp.T2D_Ahola_Olli cor_assoc do_metabowas find_BBMRI_names get.p get.s getECE getMCE getvol hist_plots hist_plots_mortality impute_miss is.sym kapmeier_scores loading loading_spin LOBOV_accuracies MetaboWAS model_coeff_heat MOLEPI_LCBC_header multi_hist NA_message pheno_barplots plattCalib_evaluation plattCalibration plot_corply plot_na_heatmap plotly_NA_message predictions_surrogates prep_data_COVID_score prep_met_for_scores QCprep QCprep_surrogates rendertable report.dim resort.on.p resort.on.s roc_surro roc_surro_subplots scatterplot_predictions startApp subset_metabolites_overlap subset_samples_miss subset_samples_sd subset_samples_sd_surrogates subset_samples_zero ttest_scores ttest_surrogates

Dependencies:abind anytime askpass assertthat backports base64enc BH boot broom bslib ca cachem callr car carData caret class cli clock cluster codetools colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table dendextend Deriv diagram digest doBy dplyr DT e1071 egg evaluate exactRankTests fansi farver fastmap fontawesome foreach fs future future.apply gclus generics ggplot2 ggpubr ggrepel ggsci ggsignif ggtext globals glue gower gridExtra gridtext gtable hardhat heatmaply highr htmltools htmlwidgets httpuv httr ipred isoband iterators jpeg jquerylib jsonlite KernSmooth km.ci KMsurv knitr labeling later lattice lava lazyeval lifecycle listenv lme4 lubridate magrittr markdown MASS Matrix MatrixModels matrixStats maxstat memoise mgcv microbenchmark mime minqa ModelMetrics modelr munsell mvtnorm nlme nloptr nnet numDeriv openssl parallelly pbkrtest permute pillar pkgconfig plotly plyr png polynom pROC processx prodlim progressr promises proxy ps purrr qap quantreg R6 rappdirs RColorBrewer Rcpp RcppEigen recipes registry reshape2 rlang rmarkdown rpart rstatix sass scales seriation shape shiny shinycssloaders shinydashboard shinyFiles shinyjs shinyWidgets sourcetools SparseM SQUAREM stringi stringr survival survminer survMisc sys tibble tidyr tidyselect timechange timeDate tinytex TSP tzdb utf8 vctrs vegan viridis viridisLite webshot withr xfun xml2 xtable yaml zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
acc_LOBOV	acc_LOBOV
T2D-score Betas	Ahola_Olli_betas
BBMRI_hist	BBMRI_hist
multi_hist	BBMRI_hist_plot
BBMRI_hist_scaled	BBMRI_hist_scaled
binarize_all_pheno	binarize_all_pheno
BMI_LDL_eGFR	BMI_LDL_eGFR
c21	c21
calculate_surrogate_scores	calculate_surrogate_scores
comp_covid_score	comp_covid_score
comp.CVD_score	comp.CVD_score
comp.mort_score	comp.mort_score
comp.T2D_Ahola_Olli	comp.T2D_Ahola_Olli
cor_assoc	cor_assoc
COVID-score betas	covid_betas
CVD-score betas	CVD_score_betas
find_BBMRI_names	find_BBMRI_names
hist_plots	hist_plots
hist_plots_mortality	hist_plots_mortality
kapmeier_scores	kapmeier_scores
LOBOV_accuracies	LOBOV_accuracies
metabolomics feature nomenclatures	metabo_names_translator
metabolomics feature subsets	metabolites_subsets
MetaboWAS	MetaboWAS
Mortality score betas	mort_betas
multi_hist	multi_hist
PARAMETERS MetaboAge	PARAM_metaboAge
PARAMETERS surrogates	PARAM_surrogates
pheno_barplots	pheno_barplots
phenotypic features names	phenotypes_names
plattCalibration	plattCalibration
plot_corply	plot_corply
plot_na_heatmap	plot_na_heatmap
prep_data_COVID_score	prep_data_COVID_score
prep_met_for_scores	prep_met_for_scores
QCprep	QCprep
QCprep_surrogates	QCprep_surrogates
roc_surro	roc_surro
roc_surro_subplots	roc_surro_subplots
scatterplot_predictions	scatterplot_predictions
startMiMIR	startApp
synthetic metabolomics dataset	synthetic_metabolic_dataset
synthetic metabolomics dataset	synthetic_phenotypic_dataset
ttest_scores	ttest_scores
ttest_surrogates	ttest_surrogates