Package: LUCIDus 2.2.1

Yinqi Zhao

LUCIDus: Latent Unknown Clustering Integrating Multi-View Data

An implementation of the LUCID model (Peng (2019) <doi:10.1093/bioinformatics/btz667>). LUCID conducts integrated clustering using exposures, omics data (and outcome as an option). An EM algorithm is implemented to estimate MLE of the LUCID model. 'LUCIDus' features integrated variable selection, incorporation of missing omics data, bootstrap inference, prediction and visualization of the model.

Authors:Yinqi Zhao [aut, cre], David Conti [ths], Jesse Goodrich [ctb], Cheng Peng [ctb]

LUCIDus_2.2.1.tar.gz
LUCIDus_2.2.1.zip(r-4.7)LUCIDus_2.2.1.zip(r-4.6)LUCIDus_2.2.1.zip(r-4.5)
LUCIDus_2.2.1.tgz(r-4.6-any)LUCIDus_2.2.1.tgz(r-4.5-any)
LUCIDus_2.2.1.tar.gz(r-4.7-any)LUCIDus_2.2.1.tar.gz(r-4.6-any)
LUCIDus_2.2.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
LUCIDus/json (API)

# Install 'LUCIDus' in R:

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

Bug tracker:https://github.com/uscbiostats/lucidus/issues

Datasets:

helix_data - HELIX data
sim_data - A simulated dataset for LUCID

On CRAN:

5.39 score 7 stars 35 scripts 544 downloads 9 exports 54 dependencies

Last updated from:44a42cf8de. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	NOTE	173
source / vignettes	OK	189
linux-release-x86_64	NOTE	164
macos-release-arm64	NOTE	149
macos-oldrel-arm64	NOTE	132
windows-devel	NOTE	122
windows-release	NOTE	111
windows-oldrel	NOTE	113
wasm-release	OK	144

Exports:boot_lucid boot.lucid est_lucid est.lucid lucid plot_lucid predict_lucid summary_lucid tune_lucid

Dependencies:base64enc boot bslib cachem cli codetools cpp11 crayon data.tree digest evaluate fastmap fontawesome foreach fs glasso glmnet glue highr hms htmltools htmlwidgets igraph iterators jquerylib jsonlite knitr lattice lifecycle magrittr Matrix mclust memoise mime mix networkD3 nnet pkgconfig prettyunits progress R6 rappdirs Rcpp RcppEigen rlang rmarkdown sass shape stringi survival tinytex vctrs xfun yaml

LUCIDus: an R package to implement integrative clustering

Rendered fromLUCIDus.Rmdusingknitr::rmarkdown

Last update: 2022-11-03
Started: 2022-11-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Inference of LUCID model based on bootstrap resampling	boot_lucid
Deprecated function boot.lucid	boot.lucid
Check missing patterns in omics data Z	check_na
Fit LUCID model to conduct integrated clustering	est_lucid
Deprecated function est.lucid	est.lucid
Impute missing data by optimizing the likelihood function	fill_data
generate bootstrp ci (normal, basic and percentile)	gen_ci
HELIX data	helix_data
I-step of LUCID	Istep_Z
Fit a lucid model for integrated analysis on exposure, outcome and multi-omics data	lucid
Visualize LUCID model through a Sankey diagram	plot_lucid
Predict cluster assignment and outcome based on LUCID model	predict_lucid
Print the output of 'est_lucid'	print.lucid
Print the output of LUCID in a nicer table	print.sumlucid
A simulated dataset for LUCID	sim_data
Summarize results of LUCID model	summary_lucid
A wrapper function to perform model selection for LUCID	tune_lucid