harmanresults {Harman} | R Documentation

## Harman results object

### 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)

[Package Harman version 1.8.0 Index]