adat-helpers {SomaDataIO}

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"))

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".

Value

\link[=getAdatVersion]{getAdatVersion()}

The key-value of the Version as a string.

\link[=getSomaScanVersion]{getSomaScanVersion()}

The key-value of the AssayVersion as a string.

\link[=getSignalSpace]{getSignalSpace()}

The key-value of the SignalSpace as a string.

\link[=checkSomaScanVersion]{checkSomaScanVersion()}

Returns NULL (invisibly) if checks pass.

\link[=getSomaScanLiftCCC]{getSomaScanLiftCCC()}

Returns a tibble of either the serum or plasma CCC between various versions of the SomaScan assay.

Author(s)

Stu Field

References

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

Examples

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")