Meta schema

Meta schema

misc_make_metadata()

Value

a Metadata object

Details

V2 version for meta data 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