Package: eclust 0.1.0

eclust: Environment Based Clustering for Interpretable Predictive Models in High Dimensional Data

Companion package to the paper: An analytic approach for interpretable predictive models in high dimensional data, in the presence of interactions with exposures. Bhatnagar, Yang, Khundrakpam, Evans, Blanchette, Bouchard, Greenwood (2017) <doi:10.1101/102475>. This package includes an algorithm for clustering high dimensional data that can be affected by an environmental factor.

Authors:Sahir Rai Bhatnagar [aut, cre]

eclust_0.1.0.tar.gz
eclust_0.1.0.zip(r-4.5)eclust_0.1.0.zip(r-4.4)eclust_0.1.0.zip(r-4.3)
eclust_0.1.0.tgz(r-4.4-any)eclust_0.1.0.tgz(r-4.3-any)
eclust_0.1.0.tar.gz(r-4.5-noble)eclust_0.1.0.tar.gz(r-4.4-noble)
eclust_0.1.0.tgz(r-4.4-emscripten)eclust_0.1.0.tgz(r-4.3-emscripten)
eclust.pdf |eclust.html✨
eclust/json (API)
NEWS

# Install 'eclust' in R:

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

Bug tracker:https://github.com/sahirbhatnagar/eclust/issues

Datasets:

simdata - Simulated Data with Environment Dependent Correlations
tcgaov - Subset of TCGA mRNA Ovarian serous cystadenocarcinoma data

On CRAN:

4.15 score 2 stars 14 scripts 244 downloads 15 exports 142 dependencies

Last updated 7 years agofrom:b75d4275dc. Checks:OK: 1 NOTE: 6. Indexed: yes.

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

Exports:r_cluster_data r_prepare_data s_generate_data s_generate_data_mars s_mars_clust s_mars_separate s_modules s_pen_clust s_pen_separate s_response s_response_mars u_cluster_similarity u_extract_selected_earth u_extract_summary u_fisherZ

Dependencies:AnnotationDbi askpass backports base64enc Biobase BiocGenerics Biostrings bit bit64 blob bslib cachem caret checkmate class cli clock cluster codetools colorspace cpp11 crayon curl data.table DBI diagram digest doParallel dplyr dynamicTreeCut e1071 evaluate fansi farver fastcluster fastmap fontawesome foreach foreign Formula fs future future.apply generics GenomeInfoDb GenomeInfoDbData ggplot2 globals glue GO.db gower gridExtra gtable hardhat highr Hmisc htmlTable htmltools htmlwidgets httr impute ipred IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice lava lifecycle listenv lubridate magrittr MASS Matrix matrixStats memoise mgcv mime ModelMetrics munsell nlme nnet numDeriv openssl pacman pander parallelly pillar pkgconfig plogr plyr png preprocessCore pROC prodlim progressr proxy purrr R6 rappdirs RColorBrewer Rcpp recipes remotes reshape2 rlang rmarkdown rpart RSQLite rstudioapi S4Vectors sass scales shape SQUAREM stringi stringr survival sys tibble tidyr tidyselect timechange timeDate tinytex tzdb UCSC.utils utf8 vctrs viridis viridisLite WGCNA withr xfun XVector yaml zlibbioc

Introduction to eclust

Sahir Rai Bhatnagar

Rendered fromeclust.Rmdusingknitr::rmarkdownon Oct 29 2024.

Last update: 2017-01-25
Started: 2016-09-20

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot Heatmap of Cluster Summaries by Exposure Status	plot.eclust
Function to generate heatmap	plot.similarity
Cluster data using environmental exposure	r_cluster_data
Prepare data for regression routines	r_prepare_data
Generate linear response data and test and training sets for simulation study	s_generate_data
Generate non linear response and test and training sets for non-linear simulation study	s_generate_data_mars
Fit MARS Models on Simulated Cluster Summaries	s_mars_clust
Fit Multivariate Adaptive Regression Splines on Simulated Data	s_mars_separate
Simulate Covariates With Exposure Dependent Correlations	s_modules
Fit Penalized Regression Models on Simulated Cluster Summaries	s_pen_clust
Fit Penalized Regression Models on Simulated Data	s_pen_separate
Generate True Response vector for Linear Simulation	s_response
Generate True Response vector for Non-Linear Simulation	s_response_mars
Simulated Data with Environment Dependent Correlations	simdata
Subset of TCGA mRNA Ovarian serous cystadenocarcinoma data	tcgaov
Cluster similarity matrix	u_cluster_similarity
Get selected terms from an earth object	u_extract_selected_earth
Calculates cluster summaries	u_extract_summary
Calculate Fisher's Z Transformation for Correlations	fisherTransform u_fisherZ