CNVreg: CNV-Profile Regression for Copy Number Variants Association Analysis with Penalized Regression

Performs copy number variants association analysis with Lasso and Weighted Fusion penalized regression. Creates a "CNV profile curve" to represent an individual’s CNV events across a genomic region so to capture variations in CNV length and dosage. When evaluating association, the CNV profile curve is directly used as a predictor in the regression model, avoiding the need to predefine CNV loci. CNV profile regression estimates CNV effects at each genome position, making the results comparable across different studies. The penalization encourages sparsity in variable selection with a Lasso penalty and encourages effect smoothness between consecutive CNV events with a weighted fusion penalty, where the weight controls the level of smoothing between adjacent CNVs. For more details, see Si (2024) <doi:10.1101/2024.11.23.624994>.

Version:	1.0
Depends:	R (≥ 4.1.0)
Imports:	stats, Matrix, doParallel, dplyr, foreach, glmnet, tidyr
Suggests:	rmarkdown, knitr, rlang, tidyverse, markdown, kableExtra, patchwork, ggplot2, withr
Published:	2025-03-10
DOI:	10.32614/CRAN.package.CNVreg
Author:	Yaqin Si [aut], Shannon T. Holloway [ctb, cre], Jung-Ying Tzeng [ctb]
Maintainer:	Shannon T. Holloway <shannon.t.holloway at gmail.com>
License:	GPL-3
NeedsCompilation:	no
Materials:	README
CRAN checks:	CNVreg results

Documentation:

Reference manual:	CNVreg.pdf
Vignettes:	Introduction to 'CNVreg' Package (source, R code)

Downloads:

Package source:	CNVreg_1.0.tar.gz
Windows binaries:	r-devel: CNVreg_1.0.zip, r-release: CNVreg_1.0.zip, r-oldrel: CNVreg_1.0.zip
macOS binaries:	r-release (arm64): CNVreg_1.0.tgz, r-oldrel (arm64): CNVreg_1.0.tgz, r-release (x86_64): CNVreg_1.0.tgz, r-oldrel (x86_64): CNVreg_1.0.tgz

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