Package: CNVreg
Type: Package
Title: CNV-Profile Regression for Copy Number Variants Association
        Analysis with Penalized Regression
Version: 1.0
Authors@R: c(person("Yaqin", "Si",email = "ysi4@ncsu.edu", role = c("aut")), 
             person("Shannon T.", "Holloway",email = "shannon.t.holloway@gmail.com", role = c("ctb", "cre")),
             person("Jung-Ying", "Tzeng",email = "jytzeng@ncsu.edu", role = c("ctb")))
Description: 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>.
License: GPL-3
Depends: R (>= 4.1.0)
VignetteBuilder: knitr
Imports: stats, Matrix, doParallel, dplyr, foreach, glmnet, tidyr
Encoding: UTF-8
NeedsCompilation: no
LazyData: true
Suggests: rmarkdown, knitr, rlang, tidyverse, markdown, kableExtra,
        patchwork, ggplot2, withr
Author: Yaqin Si [aut],
  Shannon T. Holloway [ctb, cre],
  Jung-Ying Tzeng [ctb]
Maintainer: Shannon T. Holloway <shannon.t.holloway@gmail.com>
RoxygenNote: 7.3.2
Collate: 'utils.R' 'probPred.R' 'linearPred.R' 'logLH.R' 'loss.R'
        'helpful_tests.R' 'ctnsSolution.R' 'rwlsSolution.R'
        'Wtsmth_Fit.R' 'nfoldSplit.R' 'WTsmth_nFold_CV.R' 'breakCNV.R'
        'datadescrip.R' 'wideDataRaw.R' 'wideFrequency.R'
        'weightMatrix.R' 'prep.R'
Packaged: 2025-03-09 16:07:45 UTC; sth45
Repository: CRAN
Date/Publication: 2025-03-10 16:50:21 UTC
Built: R 4.6.0; ; 2026-04-29 14:08:31 UTC; unix
