Package 'SeuratData'

Get list of available datasets

Description

Get list of available datasets

Usage

AvailableData()

Value

A dataframe with available Seurat datasets. Rownames of the dataframe are the actual package names

Dataset

Name of dataset, usable for other functions in SeuratData (eg. InstallData)

Version

Version of dataset, generally corresponds to version of Seurat dataset was built with

Installed

Is the dataset installed?

InstalledVersion

Version of dataset installed, NA if not installed

Other columns are extra metadata, and may change as new datasets are made available

See Also

InstallData InstalledData RemoveData UpdateData

Examples

AvailableData()

---

Install a dataset

Description

Install a dataset

Usage

InstallData(ds, force.reinstall = FALSE, ...)

Arguments

ds	List of datasets to install
force.reinstall	Force reinstall already installed packages
...	Extra parameters passed to install.packages

Value

Invisible NULL

See Also

AvailableData InstalledData RemoveData UpdateData

Examples

## Not run: 
InstallData('pbmc3k')

## End(Not run)

---

Get a list of installed datasets

Description

Get a list of installed datasets

Usage

InstalledData()

Value

A dataframe with installed Seurat datasets. Rownames of the dataframe are the actual package names

Dataset

Name of dataset, usable for other functions in SeuratData (eg. InstallData)

Version

Version of dataset, generally corresponds to version of Seurat dataset was built with

Installed

Is the dataset installed?

InstalledVersion

Version of dataset installed

Other columns are extra metadata, and may change as new datasets are made available

See Also

AvailableData InstallData RemoveData UpdateData

Examples

InstalledData()

---

Modularly load a dataset

Description

Modularly load a dataset

Usage

LoadData(ds, type = "default")

Arguments

ds	Optional name of dataset to load
type	How to load the Seurat object; choose from either 'default' for the default dataset or any dataset listed in the other.datasets section of the data manifest

Value

A Seurat object with the dataset asked for

See Also

data

---

Load the reference RDS files

Description

Read in a reference Seurat object and annoy index. This function can read from a file path. In order to read properly, there must be the following files:

• “ref.Rds” for the downsampled reference Seurat object (for mapping)

• “idx.annoy” for the nearest-neighbor index object

Usage

LoadReference(path)

Arguments

path	Pathto the two RDS files

Value

A list with two entries:

map

The downsampled reference Seurat object (for mapping)

plot

The reference Seurat object (for plotting)

---

Remove a dataset

Description

Remove a dataset

Usage

RemoveData(ds, lib)

Arguments

ds	List of datasets to remove
lib	a character vector giving the library directories to remove the packages from. If missing, defaults to the first element in .libPaths().

See Also

AvailableData InstallData InstalledData UpdateData

Examples

## Not run: 
RemoveData('pbmc3k')

## End(Not run)

---

Update datasets

Description

Update datasets

Usage

UpdateData(ask = TRUE, lib.loc = NULL)

Arguments

ask	logical indicating whether to ask the user to select packages before they are downloaded and installed, or the character string "graphics", which brings up a widget to allow the user to (de-)select from the list of packages which could be updated. (The latter value only works on systems with a GUI version of select.list, and is otherwise equivalent to ask = TRUE.)
lib.loc	character vector describing the location of R library trees to search through (and update packages therein), or NULL for all known trees (see .libPaths).

Value

Invisible NULL

See Also

AvailableData InstallData InstalledData RemoveData

Examples

## Not run: 
UpdateData(ask = FALSE)

## End(Not run)

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