DepMapFiles: DepMap Dataset and Files

In UCLouvain-CBIO/depmap: Cancer Dependency Map Data Package

DepMap Dataset and Files

Description

Two tibbles are provided that give access to DepMap data, as shared by the Broad Institute's DepMap project on Figshare (https://figshare.com/authors/Broad_DepMap/5514062).

- The [dmsets()] function returns a tibble with DepMap datasets. Each dataset is described by its title, its unique identifier, the number of files it contains, the Figshare URL, and a 'DepMapDataset' object that contains further details of the dataset.

- The [dmfiles()] function returns a tibble with DepMap files. Each file is described by its dataset identifier, its own unique identifier, its name, size (in bytes), a download URL, md5 hash and mime type.

- Depmap data files can be downloaded with the [dmget()] function, that takes as input a tibble or data.frame of depmap files such as 'dmfiles'. Files are downloaded and automatically in the package's central cache. See [dmCache()].

Usage

DepMapDataset(id)

DepMapFiles(x)

dmFileNames(object)

dmTitle(object)

dmNumFiles(object)

dmget(dmtab, cache = dmCache())

dmfiles()

dmsets()

Arguments

id	'numeric()' with one or multiple DepMap dataset identifier(s). Note that 'id' is converted to an integer. Missing values are not permitted.
x	either an 'numeric()' that will be passed to 'DepMapDataset' or an instance (or list of) 'DepMapDataset'.
object	an instance of class 'DepMapDataset'.
dmtab	A 'tibble' or 'data.frame' containing the file to be downloaded, such as [dmfiles()], or created by [DepMapFiles()]. If is expected to contain the '"name"', '"id"' and '"dowload_url"' variables.
cache	Object of class [BiocFileCache()]. Default is to use the central 'depmap' cache returned by [dmCache()], but users can use their own cache.

Details

The 'DepMapDataset' class stores the informtion describing a depmap dataset, as stored on Figshare (articles, as it's called there). The [DepMapDataset()] constructor requires one or multiple dataset identifiers and returns one or a list of instances.

The following accessors are available: - [dmFileNames()] returns the dataset's filenames. - [dmTitle()] returns the dataset's title. - [dmNumFiles()] returns the number of files in the dataset.

(These are used to construct the main depmap dataset tibble.)

A tibble describing the files in depmap dataset can be cretated with the [DepMapFiles()] function. It either takes one or multiple dataset idenifiers, or one or a list of 'DepMapDataset' instances

The [DepMapDataset()] and [DepMapFiles()] functions are mostly used internally, to create the 'dmsets' and 'dmfiles' tibbles. If a more recent dataset is available on Figshare and not (yet) in the 'depmap' package, a user might create the depmap files table to download the files, and/or open a [GitHub issue](https://github.com/UCLouvain-CBIO/depmap) for the new data to be added by the maintainer(s).

All the information is retrieved from Figshare using their API, as described at https://docs.figshare.com.

Adding new datasets

Adding new datasets is simple. Once a new dataset (or Article, as called on Figshare) has been identified on the Broad Institute's [DepMap project on Figshare](https://figshare.com/authors/Broad_DepMap/5514062), one needs to add the dataset's URL to the 'depmapURLs' vector in ['inst/extdata/make-dmfiles.R'](https://github.com/UCLouvain-CBIO/depmap/blob/master/inst/scripts/make-dmfiles.R), and re-run the script to update the 'dmsets.rds.' and 'dmfiles.rds' files in 'inst/extdata'.

Feel free to send a GitHub pull request or open a [GitHub issue](https://github.com/UCLouvain-CBIO/depmap) for the new data to be added by the maintainer(s).

Author(s)

Laurent Gatto

Examples

## The depmap datasets
dmsets

## The depmap files
dmfiles

############################################################
## Mostly for internal use, or to update/generate the depmap
## dataset and files tables.

## One dataset identifier: 24667905
my_dmset <- DepMapDataset(24667905)
my_dmset

## Multiple dataset identifiers
my_dmsets <- DepMapDataset(c(24667905, 22765112))
my_dmsets

## Create the files table from one or dataset multiple dataset
## identifiers

DepMapFiles(24667905)
DepMapFiles(my_dmset)

DepMapFiles(c(24667905, 22765112))
DepMapFiles(my_dmsets)

UCLouvain-CBIO/depmap documentation built on Aug. 18, 2024, 9:46 p.m.