Prepare GDC manifest file for bulk download

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)
#> # A tibble: 3 × 43
#>   id           proportion_reads_map…¹ access wgs_coverage proportion_base_mism…²
#>   <chr>                         <dbl> <chr>  <chr>                         <dbl>
#> 1 6adbeaf6-a0…                   1.00 contr… 10x-25x                     0.00710
#> 2 025fb946-1d…                  NA    open   NA                         NA      
#> 3 c9f1250c-d4…                  NA    contr… NA                         NA      
#> # ℹ abbreviated names: ¹​proportion_reads_mapped, ²​proportion_base_mismatch
#> # ℹ 38 more variables: contamination_error <dbl>, tumor_ploidy <dbl>,
#> #   acl_1 <chr>, type <chr>, platform <chr>, msi_score <dbl>,
#> #   state_comment <lgl>, created_datetime <chr>, md5sum <chr>,
#> #   updated_datetime <chr>, error_type <lgl>, pairs_on_diff_chr <int>,
#> #   state <chr>, data_format <chr>, tumor_purity <dbl>, total_reads <int>,
#> #   proportion_coverage_30x <dbl>, file_name <chr>, mean_coverage <dbl>, …