harmanresults: Harman results object

In Harman: The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Description

The S3 object returned after running harman.

Details

harmanresults 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.

Slots

factors

A data.frame of the expt and batch vectors.

parameters

The harman runtime parameters. See harman for details.

stats

Confidence intervals and the degree of correction for each pricipal component.

center

The centering vector returned by prcomp with center=TRUE.

rotation

The matrix of eigenvectors (by column) returned from prcomp.

original

The original PC scores returned by prcomp.

corrected

The harman corrected PC scores.

See Also

harman, reconstructData, pcaPlot, arrowPlot

Examples

## 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)

Harman documentation built on Nov. 8, 2020, 7:50 p.m.