tests/testthat/_snaps/parseHeader.md

parseHeader() correctly parses header information of an ADAT

Code
  header
Output
  $Header.Meta
  $Header.Meta$HEADER
  $Header.Meta$HEADER$AdatId
  [1] "GID-1234-56-7890-abcdef"
  attr(,"raw_key")
  [1] "!AdatId"

  $Header.Meta$HEADER$Version
  [1] "1.2"
  attr(,"raw_key")
  [1] "!Version"

  $Header.Meta$HEADER$AssayType
  [1] "PharmaServices"
  attr(,"raw_key")
  [1] "!AssayType"

  $Header.Meta$HEADER$AssayVersion
  [1] "V4"
  attr(,"raw_key")
  [1] "!AssayVersion"

  $Header.Meta$HEADER$AssayRobot
  [1] "Fluent 1 L-307"
  attr(,"raw_key")
  [1] "!AssayRobot"

  $Header.Meta$HEADER$Legal
  [1] "Experiment details and data have been processed to protect Personally Identifiable Information (PII) and comply with existing privacy laws."
  attr(,"raw_key")
  [1] "!Legal"

  $Header.Meta$HEADER$CreatedBy
  [1] "PharmaServices"
  attr(,"raw_key")
  [1] "!CreatedBy"

  $Header.Meta$HEADER$CreatedDate
  [1] "2020-07-25"
  attr(,"raw_key")
  [1] "!CreatedDate"

  $Header.Meta$HEADER$EnteredBy
  [1] "Technician2"
  attr(,"raw_key")
  [1] "!EnteredBy"

  $Header.Meta$HEADER$GeneratedBy
  [1] "Px (Build:  : ), Canopy_0.1.1"
  attr(,"raw_key")
  [1] "!GeneratedBy"

  $Header.Meta$HEADER$StudyMatrix
  [1] "EDTA Plasma"
  attr(,"raw_key")
  [1] "!StudyMatrix"

  $Header.Meta$HEADER$Title
  [1] "Example Adat Set001, Example Adat Set002"
  attr(,"raw_key")
  [1] "!Title"


  $Header.Meta$COL_DATA
  $Header.Meta$COL_DATA$Name
   [1] "SeqId"                                
   [2] "SeqIdVersion"                         
   [3] "SomaId"                               
   [4] "TargetFullName"                       
   [5] "Target"                               
   [6] "UniProt"                              
   [7] "EntrezGeneID"                         
   [8] "EntrezGeneSymbol"                     
   [9] "Organism"                             
  [10] "Units"                                
  [11] "Type"                                 
  [12] "Dilution"                             
  [13] "PlateScale_Reference"                 
  [14] "CalReference"                         
  [15] "Cal_Example_Adat_Set001"              
  [16] "ColCheck"                             
  [17] "CalQcRatio_Example_Adat_Set001_170255"
  [18] "QcReference_170255"                   
  [19] "Cal_Example_Adat_Set002"              
  [20] "CalQcRatio_Example_Adat_Set002_170255"
  attr(,"raw_key")
  [1] "!Name"

  $Header.Meta$COL_DATA$Type
   [1] "String" "String" "String" "String" "String" "String" "String" "String"
   [9] "String" "String" "String" "String" "String" "String" "String" "String"
  [17] "String" "String" "String" "String"
  attr(,"raw_key")
  [1] "!Type"


  $Header.Meta$ROW_DATA
  $Header.Meta$ROW_DATA$Name
   [1] "PlateId"                "PlateRunDate"           "ScannerID"             
   [4] "PlatePosition"          "SlideId"                "Subarray"              
   [7] "SampleId"               "SampleType"             "PercentDilution"       
  [10] "SampleMatrix"           "Barcode"                "Barcode2d"             
  [13] "SampleName"             "SampleNotes"            "AliquotingNotes"       
  [16] "SampleDescription"      "AssayNotes"             "TimePoint"             
  [19] "ExtIdentifier"          "SsfExtId"               "SampleGroup"           
  [22] "SiteId"                 "TubeUniqueID"           "CLI"                   
  [25] "HybControlNormScale"    "RowCheck"               "NormScale_20"          
  [28] "NormScale_0_005"        "NormScale_0_5"          "ANMLFractionUsed_20"   
  [31] "ANMLFractionUsed_0_005" "ANMLFractionUsed_0_5"   "Age"                   
  [34] "Sex"                   
  attr(,"raw_key")
  [1] "!Name"

  $Header.Meta$ROW_DATA$Type
   [1] "character" "character" "character" "character" "double"    "double"   
   [7] "character" "character" "integer"   "character" "logical"   "character"
  [13] "logical"   "logical"   "logical"   "logical"   "logical"   "logical"  
  [19] "logical"   "logical"   "logical"   "logical"   "logical"   "logical"  
  [25] "double"    "character" "double"    "double"    "double"    "double"   
  [31] "double"    "double"    "integer"   "character"
  attr(,"raw_key")
  [1] "!Type"


  $Header.Meta$TABLE_BEGIN
  [1] "single_sample.adat"


  $file_specs
  $file_specs$empty_adat
  [1] FALSE

  $file_specs$table_begin
  [1] 20

  $file_specs$col_meta_start
  [1] 21

  $file_specs$col_meta_shift
  [1] 35

  $file_specs$data_begin
  [1] 41

  $file_specs$old_adat
  [1] FALSE


  $row_meta
   [1] "PlateId"                "PlateRunDate"           "ScannerID"             
   [4] "PlatePosition"          "SlideId"                "Subarray"              
   [7] "SampleId"               "SampleType"             "PercentDilution"       
  [10] "SampleMatrix"           "Barcode"                "Barcode2d"             
  [13] "SampleName"             "SampleNotes"            "AliquotingNotes"       
  [16] "SampleDescription"      "AssayNotes"             "TimePoint"             
  [19] "ExtIdentifier"          "SsfExtId"               "SampleGroup"           
  [22] "SiteId"                 "TubeUniqueID"           "CLI"                   
  [25] "HybControlNormScale"    "RowCheck"               "NormScale_20"          
  [28] "NormScale_0_005"        "NormScale_0_5"          "ANMLFractionUsed_20"   
  [31] "ANMLFractionUsed_0_005" "ANMLFractionUsed_0_5"   "Age"                   
  [34] "Sex"


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SomaDataIO documentation built on April 4, 2025, 2:14 a.m.