Remove missing cells or features from liger object

Usage

removeMissing(
  object,
  orient = c("both", "feature", "cell"),
  minCells = NULL,
  minFeatures = NULL,
  useDatasets = NULL,
  newH5 = TRUE,
  filenameSuffix = "removeMissing",
  verbose = getOption("ligerVerbose", TRUE),
  ...
)

removeMissingObs(
  object,
  slot.use = NULL,
  use.cols = TRUE,
  verbose = getOption("ligerVerbose", TRUE)
)

Arguments

object: liger object
orient: Choose to remove non-expressing features ("feature"), empty barcodes ("cell"), or both of them ("both"). Default "both".
minCells: Keep features that are expressed in at least this number of cells, calculated on a per-dataset base. A single value for all datasets or a vector for each dataset. Default NULL only removes none expressing features.
minFeatures: Keep cells that express at least this number of features, calculated on a per-dataset base. A single value for all datasets or a vector for each dataset. Default NULL only removes none expressing cells.
useDatasets: A character vector of the names, a numeric or logical vector of the index of the datasets to be processed. Default NULL removes empty entries from all datasets.
newH5: Logical, whether to create a new H5 file on disk for each H5-based dataset on subset. Default TRUE
filenameSuffix: When subsetting H5-based datasets to new H5 files, this suffix will be added to all the filenames. Default "removeMissing".
verbose: Logical. Whether to show information of the progress. Default getOption("ligerVerbose") or TRUE if users have not set.
...: Arguments passed to subsetLigerDataset
slot.use: Deprecated. Always look at rawData slot of inner ligerDataset objects.
use.cols: Deprecated. Previously means "treating each column as a cell" when TRUE, now means orient="cell".

Value

Updated (subset) object.

Note

removeMissingObs will be deprecated. removeMissing covers and expands the use case and should be easier to understand.

Examples

# The example dataset does not contain non-expressing genes or empty barcodes
pbmc <- removeMissing(pbmc)