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: 2026-10-20 11:06:10 UTC; root
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: https://cran.r-universe.dev
Date/Publication: 2026-06-16 11:39:24 UTC
RemoteUrl: https://github.com/cran/slideimp
RemoteRef: HEAD
RemoteSha: dfe3063fde4e7e8b0415aa23c1d99256cc77d6d1