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CellGraphAssay Methods

CellGraphAssay-methods.Rd

Methods for CellGraphAssay objects for generics defined in other packages

Usage

# S3 method for CellGraphAssay
RenameCells(object, new.names = NULL, ...)

# S4 method for CellGraphAssay
show(object)

# S3 method for CellGraphAssay
subset(x, features = NULL, cells = NULL, ...)

# S3 method for CellGraphAssay
merge(
  x = NULL,
  y = NULL,
  merge.data = TRUE,
  add.cell.ids = NULL,
  collapse = TRUE,
  ...
)

Arguments

object

A CellGraphAssay or a CellGraphAssay5 object

new.names

A character vector with new cell IDs. The length of the vector must be equal to the number of cells in the object and the names must be unique.

...

Arguments passed to other methods

x

A CellGraphAssay object

features

Feature names

cells

Cell names

y

A CellGraphAssay object or a list of CellGraphAssay objects

merge.data

Merge the data slots instead of just merging the counts (which requires renormalization); this is recommended if the same normalization approach was applied to all objects

add.cell.ids

A character vector with sample names

collapse

If TRUE, merge layers of the same name together

Functions

  • RenameCells(CellGraphAssay): Rename cell IDs of a CellGraphAssay object

  • show(CellGraphAssay): Show method for CellGraphAssay objects

  • subset(CellGraphAssay): Subset a CellGraphAssay object

  • merge(CellGraphAssay): Merge two or more CellGraphAssay objects together