Subset ligerDataset object — subsetLigerDataset • rliger

This function subsets a ligerDataset object with valid feature and cell indices. For HDF5 based object, options are available for subsetting data into memory or a new on-disk H5 file. Feature and cell subscription is always based on the size of rawData. Therefore, the feature subsetting on scaled data, which usually contains already a subset of features, will select the intersection between the wanted features and the set available from scaled data.

Usage

subsetLigerDataset(
  object,
  featureIdx = NULL,
  cellIdx = NULL,
  useSlot = NULL,
  newH5 = TRUE,
  filename = NULL,
  filenameSuffix = NULL,
  chunkSize = 1000,
  verbose = getOption("ligerVerbose", TRUE),
  returnObject = TRUE,
  ...
)

subsetH5LigerDataset(
  object,
  featureIdx = NULL,
  cellIdx = NULL,
  useSlot = NULL,
  newH5 = TRUE,
  filename = NULL,
  filenameSuffix = NULL,
  chunkSize = 1000,
  verbose = getOption("ligerVerbose", TRUE),
  returnObject = TRUE
)

subsetMemLigerDataset(
  object,
  featureIdx = NULL,
  cellIdx = NULL,
  useSlot = NULL,
  returnObject = TRUE
)

Arguments

object: ligerDataset object. HDF5 based object if using subsetH5LigerDataset, in-memory data for subsetMemLigerDataset.
featureIdx: Character, logical or numeric index that can subscribe features. Missing or NULL for all features.
cellIdx: Character, logical or numeric index that can subscribe cells. Missing or NULL for all cells.
useSlot: The slot(s) to only consider. Choose one or more from "rawData", "normData" and "scaleData". Default NULL subsets the whole object including analysis result matrices.
newH5: Whether to create a new H5 file on disk for the subset dataset if object is HDF5 based. TRUE writes a new one, FALSE returns in memory data.
filename: Filename of the new H5 file if being created. Default NULL adds suffix ".subset_{yymmdd_HHMMSS}.h5" to the original name.
filenameSuffix: Instead of specifying the exact filename, set a suffix for the new files so the new filename looks like original.h5.[suffix].h5. Default NULL.
chunkSize: Integer. Number of maximum number of cells in each chunk, Default 1000.
verbose: Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
returnObject: Logical, whether to return a ligerDataset object for result. Default TRUE. FALSE returns a list containing requested values.
...: Arguments passed to subsetH5LigerDataset

Value

Subset object

Examples

ctrl <- dataset(pbmc, "ctrl")
ctrl.small <- subsetLigerDataset(ctrl, cellIdx = 1:5)
ctrl.tiny <- ctrl[1:5, 1:5]