dot-CreateStdAssay: Generic Assay Creation

In SeuratObject: Data Structures for Single Cell Data

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",
  ...
)

## Default S3 method:
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "counts",
  ...
)

## S3 method for class '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 class 'Matrix'
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "counts",
  ...
)

## S3 method for class 'matrix'
.CreateStdAssay(
  counts,
  min.cells = 0,
  min.features = 0,
  cells = NULL,
  features = NULL,
  transpose = FALSE,
  type = "Assay5",
  layer = "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

Value

An object of class type with a layer named layer containing the data found in counts

SeuratObject documentation built on Nov. 18, 2023, 1:06 a.m.