Meta schema
Examples
# show schema (you can still provide customized one)
# empty beause they are all NULL
Metadata()
# show schema
Metadata()$show(TRUE)
#> experimental_strategy :
#> library_id :
#> platform :
#> platform_unit_id :
#> file_segment_number :
#> quality_scale :
#> paired_end :
#> data_format :
#> file_extension :
#> reference_genome :
#> data_type :
#> data_subtype :
#> analysis_uuid :
#> gdc_file_uuid :
#> access_level :
#> investigation :
#> case_id :
#> case_uuid :
#> gender :
#> race :
#> ethnicity :
#> primary_site :
#> disease_type :
#> age_at_diagnosis :
#> vital_status :
#> days_to_death :
#> sample_id :
#> sample_uuid :
#> sample_type :
#> aliquot_id :
#> aliquot_uuid :
# or
names(Metadata()$asList(TRUE))
#> [1] "experimental_strategy" "library_id" "platform"
#> [4] "platform_unit_id" "file_segment_number" "quality_scale"
#> [7] "paired_end" "data_format" "file_extension"
#> [10] "reference_genome" "data_type" "data_subtype"
#> [13] "analysis_uuid" "gdc_file_uuid" "access_level"
#> [16] "investigation" "case_id" "case_uuid"
#> [19] "gender" "race" "ethnicity"
#> [22] "primary_site" "disease_type" "age_at_diagnosis"
#> [25] "vital_status" "days_to_death" "sample_id"
#> [28] "sample_uuid" "sample_type" "aliquot_id"
#> [31] "aliquot_uuid"
# returned meta field is actually define as function too, direclty
# call them will give you details
platform()
#> -- Platform --
#> data : NA
#> name : Platform
#> description : The version (manufacturer, model, etc.) of the
#> technology that was used sequencing or assaying.
#> See NCI Thesaurus Code: C45378.
#> category : File
#> locked : FALSE
#> type :
#> suggested_values : Affymetrix SNP Array 6.0 / Illumina HiSeq / Illumina Human Methylation 450 / Illumina GA / MDA_RPPA_Core / BCR Record / Hospital Record / Illumina Human Methylation 27 / ABI capillary sequencer / AgilentG4502A_07_3 / HG-CGH-244A / HG-CGH-415K_G4124A / CGH-1x1M_G4447A / Illumina MiSeq / HT_HG-U133A / Illumina Human 1M Duo / H-miRNA_8x15Kv2 / Illumina HumanHap550 / H-miRNA_8x15K / AgilentG4502A_07_2 / HuEx-1_0-st-v2 / ABI SOLiD / Complete Genomics / HG-U133_Plus_2 / Illumina DNA Methylation OMA003 CPI / Illumina DNA Methylation OMA002 CPI / AgilentG4502A_07_1 / Ion Torrent PGM / Affymetrix U133 Plus 2 / LS 454 / HiSeq X Ten / Mixed platforms / Illumina / Helicos / PacBio
#> regex : ^.{0,128}$
#> regexErrMsg : The Platform can contain maximum 128 characters
paired_end()
#> -- Paired-end --
#> data : NA
#> name : Paired-end
#> description : For paired-end sequencing, this value determines the
#> end of the fragment sequenced. For single-end
#> sequencing no value is needed.
#> category : File
#> locked : FALSE
#> type :
#> suggested_values : NA / 1 / 2
#> regex :
#> regexErrMsg :
quality_scale()
#> -- Quality scale --
#> data : NA
#> name : Quality scale
#> description : For raw reads, this value denotes the sequencing"
#> technology and quality format. For BAM and SAM
#> files, this value should always be 'Sanger'.
#> category : File
#> locked : FALSE
#> type :
#> suggested_values : NA / sanger / illumina13 / illumina15 / illumina18 / solexa
#> regex :
#> regexErrMsg :
# check their suggested value and construct your metadata
Metadata(platform = "Affymetrix SNP Array 6.0", paired_end = 1, quality_scale = "sanger")
#> platform : Affymetrix SNP Array 6.0
#> quality_scale : sanger
#> paired_end : 1