Nothing
preProcessAdat
applies default arguments as expectedCode
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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