embed_linear: Compute a linear embedding over a 'TourExperiment' object.
In sa-lee/sneezy: Interactively explore non-linear projections like t-SNE

Compute a linear embedding over a TourExperiment object.

embed_linear(.data, num_comp, .on = NULL, center = TRUE,
  scale = FALSE, .subset = NULL,
  .parallel = BiocParallel::SerialParam(), .engine)

## S4 method for signature 'missing'
embed_linear(.data, num_comp, .on = NULL,
  center = TRUE, scale = FALSE, .subset = NULL,
  .parallel = BiocParallel::SerialParam(), .engine)

## S4 method for signature 'BiocSingularParam'
embed_linear(.data, num_comp, .on = NULL,
  center = TRUE, scale = FALSE, .subset = NULL,
  .parallel = BiocParallel::SerialParam(), .engine)

`.data`	A `TourExperiment()` object
`num_comp`	Number of components to retain
`.on`	The named element in `.data` to compute the PCA (default is NULL which is the first assay in `.data`.
`center`	Should columns be centered? Default = TRUE
`scale`	Should columns be scaled to unit variance?
`.subset`	Restrict linear embedding to run on a subset of rows. (Default = NULL).
`.parallel`	A 'BiocParallel::BPPARAM()“ object, default is to compute in serial.
`.engine`	How to compute the embedding. If missing, defaults to `pca_exact()`.

This function is a wrapper to BiocSingular::runPCA(), with additions for computing on parts of TourExperiment object. This function always returns a TourExperiment with the reducedDim slot updated with SingleCellExperiment::LinearEmbeddingMatrix containing the sample factors, loadings, and factor data from the principal components.

sa-lee/sneezy documentation built on Nov. 25, 2019, 12:38 p.m.