.CreateStdAssay: Generic Assay Creation

Description

Create an assay object; runs a standardized filtering scheme that works regardless of the direction of the data (eg. cells as columns and features as rows or vice versa) and creates an assay object based on the initialization scheme defined for StdAssay-derived class type

Usage

.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  ...
)
# S3 method for default
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "counts",
  ...
)
# S3 method for list
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  csum = Matrix::colSums,
  fsum = Matrix::rowSums,
  ...
)
# S3 method for Matrix
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "counts",
  ...
)
# S3 method for matrix
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "counts",
  ...
)

Value

An object of class type with a layer named layer

containing the data found in counts

Arguments

counts: A two-dimensional expression matrix
min.cells: Include features detected in at least this many cells; will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff
min.features: Include cells where at least this many features are detected
cells: Vector of cell names
features: Vector of feature names
type: Type of assay object to create; must be the name of a class that's derived from StdAssay
...: Extra parameters passed to new for assay creation; used to set slots not defined by StdAssay
layer: Name of layer to store counts as
csum: Function for calculating cell sums
fsum: Function for calculating feature sums