Accessors and mutators (getters and setters) for objects of class
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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)
An object of class
Variables passed to and from from other methods.
Either samples or sequences.
Value to set the attribute to.
Logical. Should "SeqId." be prepended to the
column names of the intensities? If
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
getSampleData returns a data table containing the sample data. That
is, the input without the intensities or attributes. There is one compulsory
Character. A unique identifer for the sample.
These columns are not compulsory for the file spec, but are always included by SomaLogic:
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".
Character or numeric. The time point identified by the customer.
Character. Cohort information provided by the customer.
Character. Lab comments about the sample condition.
Character. Lab comments about assay adverse events.
Common optional columns:
Character. Identifier for the plate. For assay experiments, this also functions as an experiment identifier.
Character. Agilent slide barcode.
Integer. Agilent subarray number from 1 to 8.
Character. Either "Sample, "QC", "Buffer" or "Calibrator".
Character. 1D Barcode of aliquot.
Character. 2D Barcode of aliquot.
Character. The laboratory that ran the experiment, applicable if subcontracted.
Character. Where multiple experiments are combined, this column can be used to ensure a unique sample ID.
Character. Identifier for the person/animal/thing being sampled.
Numeric. Hybridization control normalization scale factor. For example, 1.23.
Numeric. Median normalization scale factor, for only the sequences diluted to 40% concentration. For example, 1.23.
Numeric. Median normalization scale factor, for only the sequences diluted to 0.005% concentration. For example, 1.23.
Numeric. Median normalization scale factor, for only the sequences diluted to 1% concentration. For example, 1.23.
Numeric. How much was the sample diluted? Either 40, 1, or 0.005.
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.
Character. Free text describing the sample.
Character. A unique identifier for every sample tube, assigned by the customer.
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.
A unique identifer for the SOMAmer reagent.
The unique name for the targeted proteins.
The following columns are optional but should always be provided by SomaLogic.
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.
Character. A description of the proteins targeted by the SOMAmer reagent, taken from 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.
Character. The Entrez Gene identifiers for the genes corresponding to the targeted proteins.
Character. The Entrez Gene symbols for the genes corresponding to the targeted proteins.
Character. What animal does the target protein refer to?
Character. Either PASS or FAIL. Did the sequence pass quality control checks?
Character. Unit of measurement for the SOMAmer reagent abundances. Should always be RFU.
Character. One of "Spuriomer", "Protein", "Hybridization Control", "Non-human Protein".
Numeric. Calibration scale factor for each plate. For example, 1.23.
Numeric. Calibration reference intensity, in RFU. For example, 543.21.
Numeric. Concentration of the diluted sample compared to the neat sample, as a percentage. Either 40, 1, or 0.005.
getMetadata return the checksum (a string) and
metadata (a list) attributes of the input.
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# 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")
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