Package: Harman 1.35.0
Jason Ross
Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique
Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.
Authors:
Harman_1.35.0.tar.gz
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Harman.pdf |Harman.html✨
Harman/json (API)
NEWS
| # Install 'Harman' in R: |
| install.packages('Harman', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:Harman-1.33.0(bioc 3.20)Harman-1.32.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
batcheffectmicroarraymultiplecomparisonprincipalcomponentnormalizationpreprocessingdnamethylationtranscriptionsoftwarestatisticalmethod
Last updated 26 days agofrom:e1dee17218. Checks:ERROR: 8 WARNING: 1. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Oct 30 2024 |
| R-4.5-win-x86_64 | ERROR | Oct 30 2024 |
| R-4.5-linux-x86_64 | WARNING | Oct 30 2024 |
| R-4.4-win-x86_64 | ERROR | Oct 30 2024 |
| R-4.4-mac-x86_64 | ERROR | Oct 30 2024 |
| R-4.4-mac-aarch64 | ERROR | Oct 30 2024 |
| R-4.3-win-x86_64 | ERROR | Oct 30 2024 |
| R-4.3-mac-x86_64 | ERROR | Oct 30 2024 |
| R-4.3-mac-aarch64 | ERROR | Oct 30 2024 |
Exports:arrowPlotclusterStatsdiscoverClusteredMethylationharmankClusterMethylationpcaPlotprcompPlotreconstructDatashiftBetas
Dependencies:Ckmeans.1d.dpmatrixStatsrbibutilsRcppRdpack
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| PCA before and after arrow plot for harman results | arrowPlot |
| Wrapper function to call the shared C/C++ library code | .callHarman callHarman |
| Compute LVR and meandiff statistics for beta values after batch correction | clusterStats |
| Detach the Harman package and its shared C/C++ library code | detachHarman |
| Discover clustered beta values | discoverClusteredMethylation |
| Harman batch correction method | harman |
| Harman results object | harmanresults |
| A Principal components prcomp function tweaked for Harman | harmanScores |
| Cluster beta values with a set value for k | kClusterMethylation |
| PCA plot for harman results | pcaPlot |
| Plot method for harman | plot.harmanresults |
| PCA plot | prcompPlot |
| Printing Harmanresults summaries. | print.summary.harmanresults |
| Reconstruct corrected data from Harman results | reconstructData |
| Shift beta values from 0 and 1 to avoid infinite M values | shiftBetas |
| Summarizing harman results. | summary.harmanresults |
