manifest: Prepare GDC manifest file for bulk download

In Bioconductor/GenomicDataCommons: NIH / NCI Genomic Data Commons Access

Prepare GDC manifest file for bulk download

Description

The manifest function/method creates a manifest of files to be downloaded using the GDC Data Transfer Tool. There are methods for creating manifest data frames from GDCQuery objects that contain file information ("cases" and "files" queries).

Usage

manifest(x, from = 0, size = count(x), ...)

## S3 method for class 'gdc_files'
manifest(x, from = 0, size = count(x), ...)

## S3 method for class 'GDCfilesResponse'
manifest(x, from = 0, size = count(x), ...)

## S3 method for class 'GDCcasesResponse'
manifest(x, from = 0, size = count(x), ...)

Arguments

x	An GDCQuery object of subclass "gdc_files" or "gdc_cases".
from	Record number from which to start when returning the manifest.
size	The total number of records to return. Default will return the usually desirable full set of records.
...	passed to PUT.

Value

A tibble, also of type "gdc_manifest", with five columns:

• id

• filename

• md5

• size

• state

Methods (by class)

• manifest(gdc_files):

• manifest(GDCfilesResponse):

• manifest(GDCcasesResponse):

Examples

gFiles = files()
shortManifest = gFiles |> manifest(size=10)
head(shortManifest,n=3)

Bioconductor/GenomicDataCommons documentation built on Oct. 31, 2024, 7 a.m.