Add lifting accessor function for Lin's CCC

- new function getLiftCCC()
- accesses the lifting correlations between
  SomaScan versions for each analyte
- fixed small bug with SomaReadr reference
  in params.R
- closes SomaLogic#88

NAMESPACE

@@ -82,6 +82,7 @@ export(getMeta)
 export(getSeqId)
 export(getSeqIdMatches)
 export(getSignalSpace)
+export(getSomaScanLiftCCC)
 export(getSomaScanVersion)
 export(getSomamerData)
 export(getSomamers)

R/adat-helpers.R

@@ -8,17 +8,17 @@
 #' [checkSomaScanVersion()] determines if the version of
 #'   is a recognized version of SomaScan.\cr
 #' \cr
-#' Table of current SomaScan Assay versions:
+#' Table of SomaScan Assay versions:
 #' \tabular{lll}{
-#'   **Version**  \tab **Name** \tab **Size** \cr
-#'   `V4`         \tab 5k       \tab 5284     \cr
-#'   `v4.1`       \tab 7k       \tab 7596     \cr
-#'   `v5.0`       \tab 11k      \tab 11083    \cr
+#'   **Version**  \tab **Commercial Name** \tab **Size** \cr
+#'   `V4`         \tab 5k                  \tab 5284     \cr
+#'   `v4.1`       \tab 7k                  \tab 7596     \cr
+#'   `v5.0`       \tab 11k                 \tab 11083    \cr
 #' }
 #'
 #' @name adat-helpers
 #' @param atts The *attributes* of a `soma_adat` object.
-#' @return Either a character string of length 1, or `NULL`.
+#' @return
 #'   \item{[getAdatVersion()]}{The key-value of the `Version` as a string.}
 #'   \item{[getSomaScanVersion()]}{The key-value of the `AssayVersion` as a string.}
 #'   \item{[checkSomaScanVersion()]}{Returns `NULL` (invisibly) if checks pass.}
@@ -94,7 +94,7 @@ getSignalSpace <- function(adat) {
 #'
 #' @rdname adat-helpers
 #' @param ver `character(1)`. The SomaScan version as a string.
-#' @note The `"v"` is case insensitive.
+#' @note The `"v"`-prefix is case insensitive.
 #' @examples
 #'
 #' is.null(checkSomaScanVersion(ver))

R/getSomaScanLiftCCC.R

@@ -0,0 +1,25 @@
+#' @rdname adat-helpers
+#'
+#' @description
+#' [getSomaScanLiftCCC()] accesses the lifting Concordance Correlation
+#'   Coefficients between various SomaScan versions.
+#'
+#' @inheritParams params
+#' @references Lin, Lawrence I-Kuei. 1989. A Concordance Correlation
+#'   Coefficient to Evaluate Reproducibility. __Biometrics__. 45:255-268.
+#' @return
+#'   \item{[getSomaScanLiftCCC()]}{Returns a tibble of either the
+#'   `serum` or `plasma` CCC between various versions of the SomaScan assay.}
+#' @examples
+#'
+#' # plasma (default)
+#' getSomaScanLiftCCC()
+#'
+#' # serum
+#' getSomaScanLiftCCC("serum")
+#' @export
+getSomaScanLiftCCC <- function(matrix = c("plasma", "serum")) {
+  matrix <- match.arg(matrix)
+  dplyr::select(lift_master, SeqId,
+                dplyr::starts_with(matrix) & dplyr::ends_with("ccc"))
+}

R/params.R

@@ -1,7 +1,7 @@
-#' Common Parameters in \pkg{SomaReadr}
+#' Common Parameters in \pkg{SomaDataIO}
 #'
 #' The parameters below are commonly used throughout
-#'   the \pkg{SomaReadr} package.
+#'   the \pkg{SomaDataIO} package.
 #'
 #' @name params
 #'
@@ -11,5 +11,8 @@
 #' @param x A `soma_adat` object (with intact attributes),
 #'   typically created using [read_adat()].
 #'
+#' @param matrix Character. A string of (usually) either 
+#'   `"serum"` or `"plasma"`.
+#'
 #' @return A `soma_adat` class object.
 NULL