getIntensities {readat} | R Documentation

## Get WideSomaLogicData attributes

### Description

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

### Usage

    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)

### Arguments

`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.

### Value

`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.

### See Also

`readAdat`

### Examples

    # 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)

    # Not run due to side effects of View
      View(intWideSamp, "Wide intensities, samples per row")

    intWideSeq <- getIntensities(                 # The transpose
      wide_soma_data,
      rowsContain = "sequences"
    )

      View(intWideSeq, "Wide intensities, seqs per row")

    # Sample data is always a data table
    sampWide <- getSampleData(wide_soma_data)

      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)

      View(intLong, "Long intensities")

    # Sample data has a different shape now
    sampLong <- getSampleData(long_soma_data)

      View(sampLong, "Long sample data")

[Package readat version 1.6.0 Index]