as.ligerDataset: Converting other classes of data to a ligerDataset object

In rliger: Linked Inference of Genomic Experimental Relationships

Converting other classes of data to a ligerDataset object

Description

Works for converting a matrix or container object to a single ligerDataset, and can also convert the modality preset of a ligerDataset. When used with a dense matrix object, it automatically converts the matrix to sparse form (dgCMatrix-class). When used with container objects such as Seurat or SingleCellExperiment, it is highly recommended that the object contains only one dataset/sample which is going to be integrated with LIGER. For multi-sample objects, please use as.liger with dataset source variable specified.

Usage

## S3 method for class 'ligerDataset'
as.ligerDataset(
  object,
  modal = c("default", "rna", "atac", "spatial", "meth"),
  ...
)

## Default S3 method:
as.ligerDataset(
  object,
  modal = c("default", "rna", "atac", "spatial", "meth"),
  ...
)

## S3 method for class 'matrix'
as.ligerDataset(
  object,
  modal = c("default", "rna", "atac", "spatial", "meth"),
  ...
)

## S3 method for class 'Seurat'
as.ligerDataset(
  object,
  modal = c("default", "rna", "atac", "spatial", "meth"),
  assay = NULL,
  ...
)

## S3 method for class 'SingleCellExperiment'
as.ligerDataset(
  object,
  modal = c("default", "rna", "atac", "spatial", "meth"),
  ...
)

as.ligerDataset(object, ...)

Arguments

object	Object.
modal	Modality setting for each dataset. Choose from "default", "rna", "atac", "spatial", "meth".
...	Additional arguments passed to createLigerDataset
assay	Name of assay to use. Default NULL uses current active assay.

Value

a liger object.

Examples

ctrl <- dataset(pbmc, "ctrl")
ctrl
# Convert the modality preset
as.ligerDataset(ctrl, modal = "atac")
rawCounts <- rawData(ctrl)
class(rawCounts)
as.ligerDataset(rawCounts)

rliger documentation built on Oct. 30, 2024, 1:07 a.m.