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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "slideimp" in publications use:'
type: software
license: GPL-2.0-or-later
title: 'slideimp: Numeric Matrices K-NN and PCA Imputation'
version: 1.2.0
doi: 10.1093/bioinformatics/btag318
identifiers:
- type: doi
  value: 10.32614/CRAN.package.slideimp
abstract: 'Fast k-nearest neighbors (K-NN) and principal component analysis (PCA)
  imputation algorithms for missing values in epigenetic data or other high-dimensional
  numeric matrices. For PCA, a locally optimal block preconditioned conjugate gradient
  (LOBPCG) eigensolver with warm starts of both the eigenblock and search direction
  is also supported. Two complementary imputation strategies are available. Group-wise
  imputation (e.g., by chromosome) is recommended for Illumina DNA methylation microarrays
  (e.g., 450K, EPIC) and other matrices with groupable columns. A sliding window approach
  for K-NN or PCA imputation is recommended only for whole-genome methylation data
  such as whole-genome bisulfite sequencing (WGBS) or Enzymatic Methyl-seq (EM-seq).
  The package also supports hyperparameter tuning via repeated cross-validation. The
  K-NN algorithm is described in: Hastie, T., Tibshirani, R., Sherlock, G., Eisen,
  M., Brown, P. and Botstein, D. (1999) "Imputing Missing Data for Gene Expression
  Arrays". The PCA imputation is an optimized reimplementation of the imputePCA()
  function from the ''missMDA'' package described in: Josse, J. and Husson, F. (2016)
  <https://doi.org/10.18637/jss.v070.i01> "missMDA: A Package for Handling Missing
  Values in Multivariate Data Analysis".'
authors:
- family-names: Pham
  given-names: Hung
  email: amser.hoanghung@gmail.com
  orcid: https://orcid.org/0000-0002-8271-9355
preferred-citation:
  type: article
  title: 'slideimp: efficient imputation of DNA methylation data'
  authors:
  - family-names: Pham
    given-names: Hung
    email: amser.hoanghung@gmail.com
    orcid: https://orcid.org/0000-0002-8271-9355
  - family-names: Lombroso
    given-names: Adam P.
  - family-names: Cevik
    given-names: Esma Cansu
  - family-names: Taylor
    given-names: Hugh S.
  - family-names: O'Donnell
    given-names: Kieran J.
  journal: Bioinformatics
  year: '2026'
  month: '6'
  volume: '42'
  issue: '6'
  doi: 10.1093/bioinformatics/btag318
  issn: 1367-4811
  start: btag318
repository: https://cran.r-universe.dev
repository-code: https://github.com/hhp94/slideimp
commit: dfe3063fde4e7e8b0415aa23c1d99256cc77d6d1
url: https://hhp94.github.io/slideimp/
date-released: '2026-06-16'
contact:
- family-names: Pham
  given-names: Hung
  email: amser.hoanghung@gmail.com
  orcid: https://orcid.org/0000-0002-8271-9355