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).
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), ...)An GDCQuery object of subclass "gdc_files" or "gdc_cases".
Record number from which to start when returning the manifest.
The total number of records to return. Default will return the usually desirable full set of records.
passed to PUT.
A tibble, also of type "gdc_manifest", with five columns:
id
filename
md5
size
state
manifest(gdc_files):
manifest(GDCfilesResponse):
manifest(GDCcasesResponse):
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: ¹proportion_reads_mapped, ²proportion_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>, …
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