Package: HarmonizR 1.10.0
Simon Schlumbohm
HarmonizR: Handles missing values and makes more data available
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. The implementation appropriately handles missing values by dissecting the input matrix into smaller matrices with sufficient data to feed the ComBat or limma algorithm. The adjusted data is returned to the user as a rebuild matrix. The implementation is meant to make as much data available as possible with minimal data loss.
Authors:
HarmonizR_1.10.0.tar.gz
HarmonizR_1.10.0.zip(r-4.7)HarmonizR_1.10.0.zip(r-4.6)HarmonizR_1.10.0.zip(r-4.5)
HarmonizR_1.10.0.tgz(r-4.6-any)HarmonizR_1.10.0.tgz(r-4.5-any)
HarmonizR_1.10.0.tar.gz(r-4.7-any)HarmonizR_1.10.0.tar.gz(r-4.6-any)
HarmonizR_1.10.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
HarmonizR/json (API)
NEWS
| # Install 'HarmonizR' in R: |
| install.packages('HarmonizR', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:HarmonizR-1.11.0(bioc 3.24)HarmonizR-1.10.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:bd9d33ce44 (on RELEASE_3_23). Checks:1 ERROR, 9 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 160 | ||
| linux-devel-x86_64 | OK | 235 | ||
| source / vignettes | OK | 252 | ||
| linux-release-x86_64 | OK | 192 | ||
| macos-release-arm64 | OK | 106 | ||
| macos-oldrel-arm64 | OK | 103 | ||
| windows-devel | OK | 153 | ||
| windows-release | OK | 210 | ||
| windows-oldrel | OK | 121 | ||
| wasm-release | OK | 136 |
Exports:harmonizR
Dependencies:abindannotateAnnotationDbiaskpassBHBiobaseBiocGenericsBiocParallelBiostringsbitbit64blobcacachemcliclustercodetoolscolorspacecpp11crayoncurlDBIDelayedArraydoParalleldplyredgeRfastmapforeachformatRfutile.loggerfutile.optionsgclusgenefiltergenericsGenomicRangesgluehmshttrIRangesiteratorsjanitorjsonliteKEGGRESTlambda.rlatticelifecyclelimmalocfitlubridatemagrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimenlmeopensslpermutepillarpkgconfigplyrpngpurrrqapR6RcppregistryrlangRSQLiteS4ArraysS4VectorsSeqinfoseriationsnakecasesnowSparseArraystatmodstringistringrSummarizedExperimentsurvivalsvasystibbletidyrtidyselecttimechangeTSPutf8vctrsveganwithrXMLxtableXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Creating a binary existence matrix | binary_matrix_reduction |
| Blocking | blocking |
| Creation of keys | build_key_list |
| Fetching batch list | fetch_batch_overview |
| Finding NAs for the sorting process | find_na |
| Format data taken from S4 | format_from_S4 |
| Format data taken from HarmonizR back to S4 | format_to_s4 |
| Main function | harmonizR |
| Jaccard-based sorting | jaccard |
| Jaccard index on zeroes (absence) | jaccard_index_absence |
| Jaccard index on ones (existence) | jaccard_index_existence |
| Reading description | read_description |
| Reading main data | read_main_data |
| Rebuilding | rebuild |
| Sorting the input data.frame | sorting |
| Splitting | splitting |
| Spotting | spotting_missing_values |
| Remove unique combinations | unique_removal |
| Visualize feature means | visual |
| Visualize sample means | visual2 |
| Visualize CV | visual3 |
