WideSomaLogicDataAttributes: Get WideSomaLogicData attributes
In graumannlab/readat: Functionality to Read and Manipulate SomaLogic ADAT files

Description Usage Arguments Value See Also Examples

Accessors and mutators (getters and setters) for objects of class WideSomaLogicData or LongSomaLogicData.

getIntensities(x, ...)

## S3 method for class 'WideSomaLogicData'
getIntensities(
  x,
  rowsContain = c("samples", "sequences"),
  reorder = FALSE,
  ...
)

## S3 method for class 'LongSomaLogicData'
getIntensities(x, ...)

## S3 method for class 'WideSomaLogicData'
as.matrix(x, ...)

getSampleData(x, ...)

## S3 method for class 'WideSomaLogicData'
getSampleData(x, ...)

## S3 method for class 'LongSomaLogicData'
getSampleData(x, ...)

getSequenceData(x)

getMetadata(x)

getChecksum(x)

setSequenceData(x, value)

setMetadata(x, value)

setChecksum(x, value)

setSampleData(x, value)

setIntensities(x, value, prependSeqIdToColNames = NA)

`x`	An object of class `WideSomaLogicData` or `LongSomaLogicData`.
`...`	Variables passed to and from from other methods.
`rowsContain`	Either samples or sequences.
`reorder`	If `TRUE`, rows are reordered by `ExtIdentifier` and columns are reordered by `SeqId`, alphabetically.
`value`	Value to set the attribute to.
`prependSeqIdToColNames`	Logical. Should "SeqId." be prepended to the column names of the intensities? If `NA`, auto-guess whether they should be.

getIntensities returns a numeric matrix of intensities for each protein. Row names are taken from the ExtIdentifier of the input. Column names are the protein sequence IDs. (If you set rowsContain = "sequences", then rows and columns and their names are swapped.)

getSampleData returns a data table containing the sample data. That is, the input without the intensities or attributes. There is one compulsory column:

ExternalId: Character. A unique identifer for the sample.

These columns are not compulsory for the file spec, but are always included by SomaLogic:

SampleId: Character. The customer's original sample identifier. This is either the same as the subject identifier, or the calibrator and buffer separated by a hyphen. For example "1234" or "PPT-09".
TimePoint: Character or numeric. The time point identified by the customer.
SampleGroup: Character. Cohort information provided by the customer.
SampleNotes: Character. Lab comments about the sample condition.
AssayNotes: Character. Lab comments about assay adverse events.

Common optional columns:

PlateId: Character. Identifier for the plate. For assay experiments, this also functions as an experiment identifier.
SlideId: Character. Agilent slide barcode.
Subarray: Integer. Agilent subarray number from 1 to 8.
SampleType: Character. Either "Sample, "QC", "Buffer" or "Calibrator".
BarCode: Character. 1D Barcode of aliquot.
Barcode2d: Character. 2D Barcode of aliquot.
SiteId: Character. The laboratory that ran the experiment, applicable if subcontracted.
SampleUniqueId: Character. Where multiple experiments are combined, this column can be used to ensure a unique sample ID.
Subject_ID: Character. Identifier for the person/animal/thing being sampled.
HybControlNormScale: Numeric. Hybridization control normalization scale factor. For example, 1.23.
NormScale_40: Numeric. Median normalization scale factor, for only the sequences diluted to 40% concentration. For example, 1.23.
NormScale_0_005: Numeric. Median normalization scale factor, for only the sequences diluted to 0.005% concentration. For example, 1.23.
NormScale_1: Numeric. Median normalization scale factor, for only the sequences diluted to 1% concentration. For example, 1.23.
PercentDilution: Numeric. How much was the sample diluted? Either 40, 1, or 0.005.
SampleMatrix: Character. Either "EDTA-Plasma", "Sodium Citrate Plasma" or "Serum". Applicable if different matrices are used with different samples in the file, otherwise use the StudyMatrix metadata value.
SampleDescription: Character. Free text describing the sample.
TubeUniqueID: Character. A unique identifier for every sample tube, assigned by the customer.
RowCheck: Character. Either "PASS" or "FAIL". Did the sample pass quality control checks?

getSequenceData returns a data table containing the sequence data. "Sequence" can be considered synonymous with "feature" or "SOMAmer reagent". The following columns are compulsory.

SeqId: A unique identifer for the SOMAmer reagent.
Target: The unique name for the targeted proteins.

The following columns are optional but should always be provided by SomaLogic.

SomaId: Character. The SomaLogic identifier for the protein target. For the 1129 and 1310 assays, there is a one-to-one correspondence between SeqId and SomaId, but in theory there is a many-to-one correspondence.
TargetFullName: Character. A description of the proteins targeted by the SOMAmer reagent, taken from UniProt.
UniProt: Character. The UniProt identifiers for the targeted proteins. Older versions of the file format may also contain the value 'Family', referring to a whole family of proteins, though this behaviour is considered deprecated.
EntrezGeneID: Character. The Entrez Gene identifiers for the genes corresponding to the targeted proteins.
EntrezGeneSymbol: Character. The Entrez Gene symbols for the genes corresponding to the targeted proteins.
Organism: Character. What animal does the target protein refer to?
ColCheck: Character. Either PASS or FAIL. Did the sequence pass quality control checks?
Units: Character. Unit of measurement for the SOMAmer reagent abundances. Should always be RFU.
Type: Character. One of "Spuriomer", "Protein", "Hybridization Control", "Non-human Protein".
Cal_*PlateId*: Numeric. Calibration scale factor for each plate. For example, 1.23.
CalReference: Numeric. Calibration reference intensity, in RFU. For example, 543.21.
Dilution: Numeric. Concentration of the diluted sample compared to the neat sample, as a percentage. Either 40, 1, or 0.005.

getCheckSum and getMetadata return the checksum (a string) and metadata (a list) attributes of the input.

readAdat

# Get the sample dataset
soma_file <- extractSampleData()
wide_soma_data <- readAdat(soma_file)

# Access its components
checksum <- getChecksum(wide_soma_data)
metadata <- getMetadata(wide_soma_data)
sequenceData <- getSequenceData(wide_soma_data)
sampleData <- getSampleData(wide_soma_data)

# Intensities of a WideSomaLogicData object are a matrix
intWideSamp <- getIntensities(wide_soma_data)
if (interactive()) {
# Not run due to side effects of View
  View(intWideSamp, "Wide intensities, samples per row")
}
intWideSeq <- getIntensities(                 # The transpose
  wide_soma_data,
  rowsContain = "sequences"
)
if (interactive()) {
  View(intWideSeq, "Wide intensities, seqs per row")
}

# Sample data is always a data table
sampWide <- getSampleData(wide_soma_data)
if (interactive()) {
  View(sampWide, "Wide sample data")
}

# For LongSomaLogicData objects, the intensities are returned
# as a data.table
long_soma_data <- reshape2::melt(wide_soma_data)
intLong <- getIntensities(long_soma_data)
if (interactive()) {
  View(intLong, "Long intensities")
}

# Sample data has a different shape now
sampLong <- getSampleData(long_soma_data)
if (interactive()) {
  View(sampLong, "Long sample data")
}