adat-helpers: Helpers to Extract Information from an ADAT

Description

Retrieve elements of the HEADER attribute of a soma_adat object:

getAdatVersion() determines the the ADAT version number from a parsed ADAT header.

getSomaScanVersion() determines the original SomaScan assay version that generated RFU measurements within a soma_adat object.

checkSomaScanVersion() determines if the version of is a recognized version of SomaScan.

Table of SomaScan assay versions:

Version	Commercial Name	Size
`V4`	5k	5284
`v4.1`	7k	7596
`v5.0`	11k	11083

getSignalSpace() determines the current signal space of the RFU values, which may differ from the original SomaScan signal space if the data have been lifted. See lift_adat() and vignette("lifting-and-bridging", package = "SomaDataIO").

getSomaScanLiftCCC() accesses the lifting Concordance Correlation Coefficients between various SomaScan versions. For more about CCC metrics see lift_adat().

Usage

getAdatVersion(x)
getSomaScanVersion(adat)
getSignalSpace(adat)
checkSomaScanVersion(ver)
getSomaScanLiftCCC(matrix = c("plasma", "serum"))

Value

getAdatVersion(): The key-value of the Version as a string.
getSomaScanVersion(): The key-value of the AssayVersion as a string.
getSignalSpace(): The key-value of the SignalSpace as a string.
checkSomaScanVersion(): Returns NULL (invisibly) if checks pass.
getSomaScanLiftCCC(): Returns a tibble of either the serum or plasma CCC between various versions of the SomaScan assay.

Arguments

x: Either a soma_adat object with intact attributes or the attributes themselves of a soma_adat object.
adat: A soma_adat object (with intact attributes), typically created using read_adat().
ver: character(1). The SomaScan version as a string. Note: the "v"-prefix is case insensitive.
matrix: Character. A string of (usually) either "serum" or "plasma".

Author

Stu Field

References

Lin, Lawrence I-Kuei. 1989. A Concordance Correlation Coefficient to Evaluate Reproducibility. Biometrics. 45:255-268.

Examples

Run this code

getAdatVersion(example_data)

attr(example_data, "Header.Meta")$HEADER$Version <- "99.9"
getAdatVersion(example_data)

ver <- getSomaScanVersion(example_data)
ver

rfu_space <- getSignalSpace(example_data)
rfu_space

is.null(checkSomaScanVersion(ver))

# plasma (default)
getSomaScanLiftCCC()

# serum
getSomaScanLiftCCC("serum")

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