Helpers to Extract Information from an ADAT — adat-helpers • SomaDataIO

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

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.

References

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

Author

Stu Field

Examples

getAdatVersion(example_data)
#> [1] "1.2"

attr(example_data, "Header.Meta")$HEADER$Version <- "99.9"
getAdatVersion(example_data)
#> [1] "99.9"

ver <- getSomaScanVersion(example_data)
ver
#> [1] "V4"

rfu_space <- getSignalSpace(example_data)
rfu_space
#> [1] "V4"

is.null(checkSomaScanVersion(ver))
#> [1] TRUE

# plasma (default)
getSomaScanLiftCCC()
#> # A tibble: 11,083 × 4
#>    SeqId    plasma_11k_to_7k_ccc plasma_11k_to_5k_ccc plasma_7k_to_5k_ccc
#>    <chr>                   <dbl>                <dbl>               <dbl>
#>  1 10000-28                0.982                0.966               0.963
#>  2 10001-7                 0.961                0.86                0.875
#>  3 10003-15                0.787                0.674               0.668
#>  4 10006-25                0.927                0.864               0.877
#>  5 10008-43                0.939                0.879               0.908
#>  6 10010-10                0.915               NA                  NA    
#>  7 10011-65                0.784                0.642               0.743
#>  8 10012-5                 0.661                0.528               0.591
#>  9 10013-34                0.824                0.76                0.744
#> 10 10014-31                0.971                0.934               0.941
#> # ℹ 11,073 more rows

# serum
getSomaScanLiftCCC("serum")
#> # A tibble: 11,083 × 4
#>    SeqId    serum_11k_to_7k_ccc serum_11k_to_5k_ccc serum_7k_to_5k_ccc
#>    <chr>                  <dbl>               <dbl>              <dbl>
#>  1 10000-28               0.977               0.97               0.967
#>  2 10001-7                0.857               0.819              0.875
#>  3 10003-15               0.759               0.761              0.774
#>  4 10006-25               0.937               0.903              0.937
#>  5 10008-43               0.951               0.915              0.925
#>  6 10010-10               0.895              NA                 NA    
#>  7 10011-65               0.748               0.515              0.741
#>  8 10012-5                0.717               0.57               0.716
#>  9 10013-34               0.86                0.716              0.778
#> 10 10014-31               0.951               0.906              0.913
#> # ℹ 11,073 more rows