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Col.Meta-doc.R
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Col.Meta-doc.R
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#' Analyte Annotations, Col.Meta, and Row Info
#'
#' In a standard SomaLogic ADAT, the section of information that
#' sits directly above the measurement data (RFU data matrix) is
#' the column meta data (`Col.Meta`), which contains detailed information
#' and annotations about the analytes, [SeqId()]s, and their targets.
#' See section below for further information about available
#' fields and their descriptions. Use [getAnalyteInfo()] to
#' obtain an object containing this information for programmatic analyses,
#' and use [getMeta()] to obtain the column names representing the
#' row-specific meta data about the samples (see section below).
#'
#' @section Col Meta (Analyte Annotations):
#' Information describing the *analytes* is found to the above
#' the data matrix in a standard SomaLogic ADAT. This information may
#' consist of the any or all of the following:
#'
#' | __Field__ | __Description__ | __Example__ |
#' | :----------------- | :------------------------------------ | :------------- |
#' | SeqId | SomaLogic sequence identifier | 2182-54_1 |
#' | SeqidVersion | Version of SOMAmer sequence | 2 |
#' | SomaId | Target identifier, of the form SLnnnnnn (8 characters in length) | SL000318 |
#' | TargetFullName | Target name curated for consistency with UniProt name | Complement C4b |
#' | Target | SomaLogic Target Name | C4b |
#' | UniProt | UniProt identifier(s) | P0C0L4 P0C0L5 |
#' | EntrezGeneID | Entrez Gene Identifier(s) | 720 721 |
#' | EntrezGeneSymbol | Entrez Gene Symbol names | C4A C4B |
#' | Organism | Protein Source Organism | Human |
#' | Units | Relative Fluorescence Units | RFU |
#' | Type | SOMAmer target type | Protein |
#' | Dilution | Dilution mix assignment | 0.01% |
#' | PlateScale_Reference | PlateScale reference value | 1378.85 |
#' | CalReference | Calibration sample reference value | 1378.85 |
#' | medNormRef_ReferenceRFU | Median normalization reference value | 490.342 |
#' | Cal_V4_\verb{<YY>_<SSS>_<PPP>}| Calibration scale factor (for given Year_Study_Plate) | 0.64 |
#' | ColCheck | QC acceptance criteria across all plates/sets | PASS |
#' | QcReference_\verb{<LLLLL>} | QC sample reference value (for given QC lot) | PASS |
#' | CalQcRatio_V4_\verb{<YY>_<SSS>_<PPP>} | Post calibration median QC ratio to reference (for given Year_Study_Plate) | 1.04 |
#'
#' @section Row Meta (Sample Annotations):
#' Information describing the *samples* is typically found to the left of
#' the data matrix in a standard SomaLogic ADAT. This information may
#' consist of clinical information provided by the client, or run-specific
#' diagnostic information included for assay quality control. Below are
#' some examples of what may be present in this section:
#'
#' | __Field__ | __Description__ | __Examples__ |
#' | :---------------- | :------------------------------------------------ | :------------- |
#' | PlateId | Plate identifier | V4-18-004_001, V4-18-004_002 |
#' | ScannerID | Scanner used to analyze slide | SG12064173, SG14374437 |
#' | PlatePosition | Location on 96 well plate (A1-H12) | A1, H12 |
#' | SlideId | Agilent slide barcode | 2.58E+11 |
#' | Subarray | Agilent subarray (1 – 8) | 1,8 |
#' | SampleId | 1st form is Subject Identifier, 2nd form (calibrators, buffers) | 2031 |
#' | SampleType | 1st form for clinical samples (Sample), 2nd form as above | Sample, QC, Calibrator, Buffer |
#' | PercentDilution | Highest concentration the SOMAmer dilution groups | 20 |
#' | SampleMatrix | Sample matrix | Plasma-PPT |
#' | Barcode | 1D Barcode of aliquot | S622225 |
#' | Barcode2d | 2D Barcode of aliquot | 1.91E+08 |
#' | SampleNotes | Assay team sample observation | Cloudy, Low sample volume, Reddish |
#' | SampleDescription | Supplemental sample information | Plasma QC 1 |
#' | AssayNotes | Assay team run observation | Beads aspirated, Leak/Hole, Smear |
#' | TimePoint | Sample time point | Baseline |
#' | ExtIdentifier | Primary key for Subarray | EXID40000000032037 |
#' | SsfExtId | Primary key for sample | EID102733 |
#' | SampleGroup | Sample group | A, B |
#' | SiteId | Collection site | SomaLogic, Covance |
#' | TubeUniqueID | Unique tube identifier | 1.12E+11 |
#' | CLI | Cohort definition identifier | CLI6006F001 |
#' | HybControlNormScale | Hybridization control scale factor | 0.948304 |
#' | RowCheck | Normalization acceptance criteria for all row scale factors | PASS, FLAG |
#' | NormScale_0_5 | Median signal normalization scale factor (0.5% mix) | 1.02718 |
#' | NormScale_0_005 | Median signal normalization scale factor (0.005% mix) | 1.119754 |
#' | NormScale_20 | Median signal normalization scale factor (20% mix) | 0.996148 |
#'
#' @examples
#' # Annotations/Col.Meta
#' tbl <- getAnalyteInfo(example_data)
#' tbl
#'
#' # Row/sample Meta
#' r_m <- getMeta(example_data)
#' head(r_m)
#'
#' # Normalization Scale Factors
#' grep("NormScale", r_m, value = TRUE)
#'
#' # adat subset
#' example_data[1:3, head(r_m)]
#' @name Col.Meta
#' @aliases colmeta annotations rowmeta
NULL