The example_data object is intended to provide existing and prospective
SomaLogic customers with example data to enable analysis preparation prior
to receipt of SomaScan data, and also for those generally curious about the
SomaScan data deliverable. It is not intended to be used as a control
group for studies or provide any metrics for SomaScan data in general.
Format
- example_data
a
soma_adatparsed viaread_adat()containing 192 samples (see below for breakdown of sample type). There are 5318 columns containing 5284 analyte features and 34 clinical meta data fields. These data have been pre-processed via the following steps:hybridization normalized (all samples)
calibrators and buffers median normalized
plate scaled
calibrated
Adaptive Normalization by Maximum Likelihood (ANML) of QC and clinical samples
Note1: The
AgeandSex(M/F) fields contain simulated values designed to contain biological signal.- ex_analytes
character string of the analyte features contained in the
soma_adatobject, derived from a call togetAnalytes().- ex_anno_tbl
a lookup table corresponding to a transposed data frame of the "Col.Meta" attribute of an ADAT, with an index key field
AptNameincluded in column 1, derived from a call togetAnalyteInfo().- ex_target_names
A lookup table mapping
SeqIdfeature names -> target names contained inexample_data. This object (or one like it) is convenient at the console via auto-complete for labeling and/or creating plot titles on the fly.
Data Description
The example_data object contains a SomaScan V4 study from healthy
normal individuals. The RFU measurements themselves and other identifiers
have been altered to protect personally identifiable information (PII),
but also retain underlying biological signal as much as possible.
There are 192 total EDTA-plasma samples across two 96-well plate runs
which are broken down by the following types:
170 clinical samples (client study samples)
10 calibrators (replicate controls for combining data across runs)
6 QC samples (replicate controls used to assess run quality)
6 Buffer samples (no protein controls)
Data Processing
The standard V4 data normalization procedure for EDTA-plasma samples was applied to this dataset. For more details on the data standardization process see the Data Standardization and File Specification Technical Note. General details are outlined above.
Examples
# S3 print method
example_data
#> ══ SomaScan Data ═════════════════════════════════════════════════════════
#> SomaScan version V4 (5k)
#> Signal Space 5k
#> Attributes intact ✓
#> Rows 192
#> Columns 5318
#> Clinical Data 34
#> Features 5284
#> ── Column Meta ───────────────────────────────────────────────────────────
#> ℹ SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt,
#> ℹ EntrezGeneID, EntrezGeneSymbol, Organism, Units, Type,
#> ℹ Dilution, PlateScale_Reference, CalReference,
#> ℹ Cal_Example_Adat_Set001, ColCheck,
#> ℹ CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,
#> ℹ Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255,
#> ℹ Dilution2
#> ── Tibble ────────────────────────────────────────────────────────────────
#> # A tibble: 192 × 5,319
#> row_names PlateId PlateRunDate ScannerID PlatePosition SlideId Subarray
#> <chr> <chr> <chr> <chr> <chr> <dbl> <dbl>
#> 1 25849580… Exampl… 2020-06-18 SG152144… H9 2.58e11 3
#> 2 25849580… Exampl… 2020-06-18 SG152144… H8 2.58e11 7
#> 3 25849580… Exampl… 2020-06-18 SG152144… H7 2.58e11 8
#> 4 25849580… Exampl… 2020-06-18 SG152144… H6 2.58e11 4
#> 5 25849580… Exampl… 2020-06-18 SG152144… H5 2.58e11 4
#> 6 25849580… Exampl… 2020-06-18 SG152144… H4 2.58e11 8
#> 7 25849580… Exampl… 2020-06-18 SG152144… H3 2.58e11 3
#> 8 25849580… Exampl… 2020-06-18 SG152144… H2 2.58e11 8
#> 9 25849580… Exampl… 2020-06-18 SG152144… H12 2.58e11 8
#> 10 25849580… Exampl… 2020-06-18 SG152144… H11 2.58e11 3
#> # ℹ 182 more rows
#> # ℹ 5,312 more variables: SampleId <chr>, SampleType <chr>,
#> # PercentDilution <int>, SampleMatrix <chr>, Barcode <lgl>,
#> # Barcode2d <chr>, SampleName <lgl>, SampleNotes <lgl>,
#> # AliquotingNotes <lgl>, SampleDescription <chr>, …
#> ══════════════════════════════════════════════════════════════════════════
# print header info
print(example_data, show_header = TRUE)
#> ══ SomaScan Data ═════════════════════════════════════════════════════════
#> SomaScan version V4 (5k)
#> Signal Space 5k
#> Attributes intact ✓
#> Rows 192
#> Columns 5318
#> Clinical Data 34
#> Features 5284
#> ── Column Meta ───────────────────────────────────────────────────────────
#> ℹ SeqId, SeqIdVersion, SomaId, TargetFullName, Target, UniProt,
#> ℹ EntrezGeneID, EntrezGeneSymbol, Organism, Units, Type,
#> ℹ Dilution, PlateScale_Reference, CalReference,
#> ℹ Cal_Example_Adat_Set001, ColCheck,
#> ℹ CalQcRatio_Example_Adat_Set001_170255, QcReference_170255,
#> ℹ Cal_Example_Adat_Set002, CalQcRatio_Example_Adat_Set002_170255,
#> ℹ Dilution2
#> ── Header Data ───────────────────────────────────────────────────────────
#> # A tibble: 35 × 2
#> Key Value
#> <chr> <chr>
#> 1 AdatId GID-1234-56-789-abcdef
#> 2 Version 1.2
#> 3 AssayType PharmaServices
#> 4 AssayVersion V4
#> 5 AssayRobot Fluent 1 L-307
#> 6 Legal Experiment details and data have been processed t…
#> 7 CreatedBy PharmaServices
#> 8 CreatedDate 2020-07-24
#> 9 EnteredBy Technician1
#> 10 ExpDate 2020-06-18, 2020-07-20
#> 11 GeneratedBy Px (Build: : ), Canopy_0.1.1
#> 12 RunNotes 2 columns ('Age' and 'Sex') have been added to th…
#> 13 ProcessSteps Raw RFU, Hyb Normalization, medNormInt (SampleId)…
#> 14 ProteinEffectiveDate 2019-08-06
#> 15 StudyMatrix EDTA Plasma
#> # ℹ 20 more rows
#> ══════════════════════════════════════════════════════════════════════════
class(example_data)
#> [1] "soma_adat" "data.frame"
# Features/Analytes
head(ex_analytes, 20L)
#> [1] "seq.10000.28" "seq.10001.7" "seq.10003.15" "seq.10006.25"
#> [5] "seq.10008.43" "seq.10011.65" "seq.10012.5" "seq.10013.34"
#> [9] "seq.10014.31" "seq.10015.119" "seq.10021.1" "seq.10022.207"
#> [13] "seq.10023.32" "seq.10024.44" "seq.10030.8" "seq.10034.16"
#> [17] "seq.10035.6" "seq.10036.201" "seq.10037.98" "seq.10040.63"
# Feature info table (annotations)
ex_anno_tbl
#> # A tibble: 5,284 × 22
#> AptName SeqId SeqIdVersion SomaId TargetFullName Target UniProt
#> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 seq.10000.28 10000-… 3 SL019… Beta-crystall… CRBB2 P43320
#> 2 seq.10001.7 10001-7 3 SL002… RAF proto-onc… c-Raf P04049
#> 3 seq.10003.15 10003-… 3 SL019… Zinc finger p… ZNF41 P51814
#> 4 seq.10006.25 10006-… 3 SL019… ETS domain-co… ELK1 P19419
#> 5 seq.10008.43 10008-… 3 SL019… Guanylyl cycl… GUC1A P43080
#> 6 seq.10011.65 10011-… 3 SL019… Inositol poly… OCRL Q01968
#> 7 seq.10012.5 10012-5 3 SL014… SAM pointed d… SPDEF O95238
#> 8 seq.10013.34 10013-… 3 SL025… Fc_MOUSE Fc_MO… Q99LC4
#> 9 seq.10014.31 10014-… 3 SL007… Zinc finger p… SLUG O43623
#> 10 seq.10015.119 10015-… 3 SL014… Voltage-gated… KCAB2 Q13303
#> # ℹ 5,274 more rows
#> # ℹ 15 more variables: EntrezGeneID <chr>, EntrezGeneSymbol <chr>,
#> # Organism <chr>, Units <chr>, Type <chr>, Dilution <chr>,
#> # PlateScale_Reference <dbl>, CalReference <dbl>,
#> # Cal_Example_Adat_Set001 <dbl>, ColCheck <chr>,
#> # CalQcRatio_Example_Adat_Set001_170255 <dbl>,
#> # QcReference_170255 <dbl>, Cal_Example_Adat_Set002 <dbl>, …
# Search via `filter()`
dplyr::filter(ex_anno_tbl, grepl("^MMP", Target))
#> # A tibble: 15 × 22
#> AptName SeqId SeqIdVersion SomaId TargetFullName Target UniProt
#> <chr> <chr> <dbl> <chr> <chr> <chr> <chr>
#> 1 seq.15419.15 15419-15 3 SL012… Matrix metall… MMP20 O60882
#> 2 seq.2579.17 2579-17 5 SL000… Matrix metall… MMP-9 P14780
#> 3 seq.2788.55 2788-55 1 SL000… Stromelysin-1 MMP-3 P08254
#> 4 seq.2789.26 2789-26 2 SL000… Matrilysin MMP-7 P09237
#> 5 seq.2838.53 2838-53 1 SL003… Matrix metall… MMP-17 Q9ULZ9
#> 6 seq.4160.49 4160-49 1 SL000… 72 kDa type I… MMP-2 P08253
#> 7 seq.4496.60 4496-60 2 SL000… Macrophage me… MMP-12 P39900
#> 8 seq.4924.32 4924-32 1 SL000… Interstitial … MMP-1 P03956
#> 9 seq.4925.54 4925-54 2 SL000… Collagenase 3 MMP-13 P45452
#> 10 seq.5002.76 5002-76 1 SL002… Matrix metall… MMP-14 P50281
#> 11 seq.5268.49 5268-49 3 SL003… Matrix metall… MMP-16 P51512
#> 12 seq.6425.87 6425-87 3 SL007… Matrix metall… MMP19 Q99542
#> 13 seq.8479.4 8479-4 3 SL000… Stromelysin-2 MMP-10 P09238
#> 14 seq.9172.69 9172-69 3 SL000… Neutrophil co… MMP-8 P22894
#> 15 seq.9719.145 9719-145 3 SL003… Matrix metall… MMP-16 P51512
#> # ℹ 15 more variables: EntrezGeneID <chr>, EntrezGeneSymbol <chr>,
#> # Organism <chr>, Units <chr>, Type <chr>, Dilution <chr>,
#> # PlateScale_Reference <dbl>, CalReference <dbl>,
#> # Cal_Example_Adat_Set001 <dbl>, ColCheck <chr>,
#> # CalQcRatio_Example_Adat_Set001_170255 <dbl>,
#> # QcReference_170255 <dbl>, Cal_Example_Adat_Set002 <dbl>,
#> # CalQcRatio_Example_Adat_Set002_170255 <dbl>, Dilution2 <dbl>
# Lookup table -> targets
# MMP-9
ex_target_names$seq.2579.17
#> [1] "Matrix metalloproteinase-9"
# gender hormone FSH
tapply(example_data$seq.3032.11, example_data$Sex, median)
#> F M
#> 3358.1 556.4
# gender hormone LH
tapply(example_data$seq.2953.31, example_data$Sex, median)
#> F M
#> 2693.8 883.6
# Target lookup
ex_target_names$seq.2953.31 # tab-completion at console
#> [1] "Luteinizing hormone"
# Sample Type/Source
table(example_data$SampleType)
#>
#> Buffer Calibrator QC Sample
#> 6 10 6 170
# Sex/Gender Variable
table(example_data$Sex)
#>
#> F M
#> 85 85
# Age Variable
summary(example_data$Age)
#> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
#> 18.00 46.00 55.00 55.66 67.00 77.00 22