harman.
factorsA data.frame of the expt and batch vectors.parametersharman
for details.statscenterprcomp with
center=TRUE.rotationprcomp.originalprcomp.correctedharmanresults is the S3 object used to store the results from
harman.
This object may be presented to summary and data exploration functions such
as plot.harmanresults
and summary.harmanresults as well as the
reconstructData function which creates a corrected matrix of
data with the batch effect removed.
harman, reconstructData,
pcaPlot, arrowPlot
## HarmanResults
library(HarmanData)
data(OLF)
expt <- olf.info$Treatment
batch <- olf.info$Batch
olf.harman <- harman(as.matrix(olf.data), expt, batch)
plot(olf.harman)
summary(olf.harman)
pcaPlot(olf.harman, pc_x=2, pc_y=3)
pcaPlot(olf.harman, pc_x=2, pc_y=3, colBy='expt', pch=1)
olf.data.corrected <- reconstructData(olf.harman)
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