# The removal of batch effects from datasets using a PCA and constrained optimisation based technique

## Documentation for package ‘Harman’ version 1.39.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

.callHarman | Wrapper function to call the shared C/C++ library code
arrowPlot | PCA before and after arrow plot for harman results
callHarman | Wrapper function to call the shared C/C++ library code
clusterStats | Compute LVR and meandiff statistics for beta values after batch correction
detachHarman | Detach the Harman package and its shared C/C++ library code
discoverClusteredMethylation | Discover clustered beta values
harman | Harman batch correction method
harmanresults | Harman results object
harmanScores | A Principal components prcomp function tweaked for Harman
kClusterMethylation | Cluster beta values with a set value for k
pcaPlot | PCA plot for harman results
plot.harmanresults | Plot method for harman
prcompPlot | PCA plot
print.summary.harmanresults | Printing Harmanresults summaries.
reconstructData | Reconstruct corrected data from Harman results
shiftBetas | Shift beta values from 0 and 1 to avoid infinite M values
summary.harmanresults | Summarizing harman results.