Type: Package
Package: slideimp
Title: Numeric Matrices K-NN and PCA Imputation
Version: 1.2.0
Authors@R: c(
    person("Hung", "Pham", , "amser.hoanghung@gmail.com", role = c("aut", "cre", "cph"),
           comment = c(ORCID = "0000-0002-8271-9355")),
    person("Posit Software, PBC", role = "cph",
           comment = "Copyright holder of code adapted from the 'carrier' package, MIT licensed")
  )
Description: 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) <doi:10.18637/jss.v070.i01> "missMDA: A
    Package for Handling Missing Values in Multivariate Data Analysis".
License: GPL (>= 2)
URL: https://github.com/hhp94/slideimp,
        https://hhp94.github.io/slideimp/
BugReports: https://github.com/hhp94/slideimp/issues
Depends: R (>= 4.3.0)
Imports: bigmemory, checkmate, cli, collapse, mirai, Rcpp, stats, utils
Suggests: knitr, missMDA, RhpcBLASctl, rmarkdown, testthat (>= 3.0.0),
        withr
LinkingTo: Rcpp, RcppArmadillo, RcppThread
VignetteBuilder: knitr
Config/Needs/website: rmarkdown
Config/roxygen2/version: 8.0.0
Config/testthat/edition: 3
Encoding: UTF-8
Language: en-US
NeedsCompilation: yes
Packaged: 2026-06-16 04:45:24 UTC; amser
Author: Hung Pham [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0002-8271-9355>),
  Posit Software, PBC [cph] (Copyright holder of code adapted from the
    'carrier' package, MIT licensed)
Maintainer: Hung Pham <amser.hoanghung@gmail.com>
Repository: CRAN
Date/Publication: 2026-06-16 06:50:02 UTC
Built: R 4.6.0; aarch64-apple-darwin23; 2026-06-16 08:10:01 UTC; unix
Archs: slideimp.so.dSYM
