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.
|Author||Josh Bowden [aut], Jason Ross [aut, cre], Yalchin Oytam [aut]|
|Date of publication||None|
|Maintainer||Jason Ross <email@example.com>|
|License||GPL-3 + file LICENCE|
arrowPlot: PCA before and after arrow plot for harman results
callHarman: Wrapper function to call the shared C/C++ library code
detachHarman: Detach the Harman package and its shared C/C++ library code
harman: Harman batch correction method
harmanresults: Harman results object
harmanScores: A Principal components prcomp function tweaked for Harman
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.