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Run PCA on GiottoDB with dbMatrix::dbMatrix support

Source: R/runPCA.R
runPCA.Rd

S3 generic for PCA that dispatches to dbMatrix::db_svd when expression data is stored as dbMatrix::dbMatrix.

Usage

runPCA(gobject, ...)

# S3 method for class 'GiottoDB'
runPCA(gobject, ...)

# S3 method for class 'giotto'
runPCA(
  gobject,
  spat_unit = NULL,
  feat_type = NULL,
  expression_values = "normalized",
  name = "pca",
  feats_to_use = "hvf",
  return_gobject = TRUE,
  ncp = 100,
  center = TRUE,
  scale_unit = FALSE,
  verbose = TRUE,
  ...
)

Arguments

gobject

A GiottoClass::giotto or GiottoDB object

...

Additional arguments passed to underlying PCA methods

spat_unit

spatial unit

feat_type

feature type

expression_values

expression values to use

name

name of PCA dimension reduction

feats_to_use

features to use for PCA

return_gobject

whether to return giotto object

ncp

number of principal components

center

center data before PCA

scale_unit

scale features before PCA

verbose

verbosity