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 |
| 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:
Downloads:
| Package source: |
CNVreg_1.0.tar.gz |
| Windows binaries: |
r-devel: not available, r-release: not available, r-oldrel: not available |
| macOS binaries: |
r-devel (arm64): not available, r-release (arm64): not available, r-oldrel (arm64): not available, r-devel (x86_64): not available, r-release (x86_64): not available, r-oldrel (x86_64): not available |
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