tests/testthat/_snaps/preProcessAdat.md

preProcessAdat applies default arguments as expected

Code
  preProcessAdat(example_data)
Message
  v 305 non-human protein features were removed.
  > 214 human proteins did not pass standard QC
  acceptance criteria and were flagged in `ColCheck`.  These features
  were not removed, as they still may yield useful information in an
  analysis, but further evaluation may be needed.
  v 6 buffer samples were removed.
  v 10 calibrator samples were removed.
  v 6 QC samples were removed.
  v 2 samples flagged in `RowCheck` did not
  pass standard normalization acceptance criteria (0.4 <= x <= 2.5)
  and were removed.
Output
  == SomaScan Data ===============================================================
       SomaScan version     V4 (5k)
       Signal Space         5k
       Attributes intact    v
       Rows                 168
       Columns              5013
       Clinical Data        34
       Features             4979
  -- Column Meta -----------------------------------------------------------------
  i SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt, EntrezGeneID,
  i EntrezGeneSymbol, Organism, Units, Type, Dilution, PlateScale_Reference,
  i CalReference, Cal_Example_Adat_Set001, ColCheck,
  i CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,
  i Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255, Dilution2
  -- Tibble ----------------------------------------------------------------------
  # A tibble: 168 x 5,014
     row_names      PlateId  PlateRunDate ScannerID PlatePosition SlideId Subarray
     <chr>          <chr>    <chr>        <chr>     <chr>           <dbl>    <dbl>
   1 258495800012_3 Example~ 2020-06-18   SG152144~ H9            2.58e11        3
   2 258495800004_7 Example~ 2020-06-18   SG152144~ H8            2.58e11        7
   3 258495800010_8 Example~ 2020-06-18   SG152144~ H7            2.58e11        8
   4 258495800003_4 Example~ 2020-06-18   SG152144~ H6            2.58e11        4
   5 258495800009_4 Example~ 2020-06-18   SG152144~ H5            2.58e11        4
   6 258495800012_8 Example~ 2020-06-18   SG152144~ H4            2.58e11        8
   7 258495800001_3 Example~ 2020-06-18   SG152144~ H3            2.58e11        3
   8 258495800004_8 Example~ 2020-06-18   SG152144~ H2            2.58e11        8
   9 258495800001_8 Example~ 2020-06-18   SG152144~ H12           2.58e11        8
  10 258495800009_8 Example~ 2020-06-18   SG152144~ H10           2.58e11        8
  # i 158 more rows
  # i 5,007 more variables: SampleId <chr>, SampleType <chr>,
  #   PercentDilution <int>, SampleMatrix <chr>, Barcode <lgl>, Barcode2d <chr>,
  #   SampleName <lgl>, SampleNotes <lgl>, AliquotingNotes <lgl>,
  #   SampleDescription <chr>, ...
  ================================================================================


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SomaDataIO documentation built on June 8, 2025, 10:13 a.m.