R/data.R

In CytoProfile: Cytokine Profiling Analysis Tool

#' Example Cytokine Profiling Data 1.
#'
#' Contains observed concentrations of cytokines and their respective treatment
#' and groups, derived from:
#'
#' @format A data frame with 297 rows and 29 columns:
#' \describe{
#'   \item{Group}{Group assigned to the subjects.}
#'   \item{Treatment}{Treatment received by subjects.}
#'   \item{Time}{Time point of the measurement.}
#'   \item{IL-17F}{Observed concentration of IL-17F cytokine.}
#'   \item{GM-CSF}{Observed concentration of GM-CSF cytokine.}
#'   \item{IFN-G}{Observed concentration of IFN-G cytokine.}
#'   \item{IL-10}{Observed concentration of IL-10 cytokine.}
#'   \item{CCL-20/MIP-3A}{Observed concentration of CCL-20/MIP-3A cytokine.}
#'   \item{IL-12/P70}{Observed concentration of IL-12/P70 cytokine.}
#'   \item{IL-13}{Observed concentration of IL-13 cytokine.}
#'   \item{IL-15}{Observed concentration of IL-15 cytokine.}
#'   \item{IL-17A}{Observed concentration of IL-17A cytokine.}
#'   \item{IL-22}{Observed concentration of IL-22 cytokine.}
#'   \item{IL-9}{Observed concentration of IL-9 cytokine.}
#'   \item{IL-1B}{Observed concentration of IL-1B cytokine.}
#'   \item{IL-33}{Observed concentration of IL-33 cytokine.}
#'   \item{IL-2}{Observed concentration of IL-2 cytokine.}
#'   \item{IL-21}{Observed concentration of IL-21 cytokine.}
#'   \item{IL-4}{Observed concentration of IL-4 cytokine.}
#'   \item{IL-23}{Observed concentration of IL-23 cytokine.}
#'   \item{IL-5}{Observed concentration of IL-5 cytokine.}
#'   \item{IL-6}{Observed concentration of IL-6 cytokine.}
#'   \item{IL-17E/IL-25}{Observed concentration of IL-17E/IL-25 cytokine.}
#'   \item{IL-27}{Observed concentration of IL-27 cytokine.}
#'   \item{IL-31}{Observed concentration of IL-31 cytokine.}
#'   \item{TNF-A}{Observed concentration of TNF-A cytokine.}
#'   \item{TNF-B}{Observed concentration of TNF-B cytokine.}
#'   \item{IL-28A}{Observed concentration of IL-28A cytokine.}
#' }
#' @source Example data compiled for cytokine profiling.
#' @references
#' Pugh GH, Fouladvand S, SantaCruz-Calvo S, Agrawal M, Zhang XD, Chen J,
#' Kern PA, Nikolajczyk BS.
#' T cells dominate peripheral inflammation in a cross-sectional analysis of
#' obesity-associated diabetes. \emph{Obesity (Silver Spring)}. 2022;30(10):
#' 1983–1994. doi:10.1002/oby.23528.
#'
#' @examples
#' data(ExampleData1)
"ExampleData1"

#' Example Cytokine Profiling Data 2.
#'
#' Contains observed concentrations of cytokines and their respective treatment
#' and groups, derived from:
#'
#' @format A data frame with 66 rows and 20 columns:
#' \describe{
#'  \item{Stimulation}{Stimulation assigned to the subjects.}
#'  \item{Group}{Group assigned to the subjects.}
#'  \item{IL-17F}{Observed concentration of IL-17F cytokine.}
#'  \item{GM-CSF}{Observed concentration of GM-CSF cytokine.}
#'  \item{IFN-G}{Observed concentration of IFN-G cytokine.}
#'  \item{IL-10}{Observed concentration of IL-10 cytokine.}
#'  \item{CCL-20}{Observed concentration of CCL-20 cytokine.}
#'  \item{IL-12}{Observed concentration of IL-12 cytokine.}
#'  \item{IL-13}{Observed concentration of IL-13 cytokine.}
#'  \item{IL-17A}{Observed concentration of IL-17A cytokine.}
#'  \item{IL-22}{Observed concentration of IL-22 cytokine.}
#'  \item{IL-9}{Observed concentration of IL-9 cytokine.}
#'  \item{IL-1B}{Observed concentration of IL-1B cytokine.}
#'  \item{IL-2}{Observed concentration of IL-2 cytokine.}
#'  \item{IL-21}{Observed concentration of IL-21 cytokine.}
#'  \item{IL-4}{Observed concentration of IL-4 cytokine.}
#'  \item{IL-5}{Observed concentration of IL-5 cytokine.}
#'  \item{IL-6}{Observed concentration of IL-6 cytokine.}
#'  \item{TNF-A}{Observed concentration of TNF-A cytokine.}
#'  \item{TNF-B}{Observed concentration of TNF-B cytokine.}
#'  }
#'
#' @source Example data compiled for cytokine profiling.
#'
#' @references
#' SantaCruz-Calvo S, Saraswat S, Hasturk H, Dawson DR, Zhang XD,
#' Nikolajczyk BS. Periodontitis and Diabetes Differentially Affect
#' Inflammation in Obesity. \emph{J Dent Res.} 2024;103(12):1313-1322.
#' doi:10.1177/00220345241280743
#'
#' @examples
#' data(ExampleData2)
"ExampleData2"

#' Example Cytokine Profiling Data 3.
#'
#' Contains observed concentrations of cytokines and their respective treatment
#' and groups, derived from:
#'
#' @format A data frame with 64 rows and 14 columns:
#' \describe{
#'  \item{Stimulation}{Stimulation assigned to the subjects.}
#'  \item{Group}{Group assigned to the subjects.}
#'  \item{GM-CSF}{Observed concentration of GM-CSF cytokine.}
#'  \item{IFN-G}{Observed concentration of IFN-G cytokine.}
#'  \item{IL-10}{Observed concentration of IL-10 cytokine.}
#'  \item{CCL-20/MIP-3A}{Observed concentration of CCL-20/MIP-3A cytokine.}
#'  \item{IL-12/P70}{Observed concentration of IL-12/P70 cytokine.}
#'  \item{IL-13}{Observed concentration of IL-13 cytokine.}
#'  \item{IL-15}{Observed concentration of IL-15 cytokine.}
#'  \item{IL-9}{Observed concentration of IL-9 cytokine.}
#'  \item{IL-1B}{Observed concentration of IL-1B cytokine.}
#'  \item{IL-21}{Observed concentration of IL-21 cytokine.}
#'  \item{IL-6}{Observed concentration of IL-6 cytokine.}
#'  \item{TNF-A}{Observed concentration of TNF-A cytokine.}
#'  }
#'
#' @source Example data compiled for cytokine profiling.
#'
#' @references
#' SantaCruz-Calvo S, Saraswat S, Hasturk H, Dawson DR, Zhang XD,
#' Nikolajczyk BS. Periodontitis and Diabetes Differentially Affect
#' Inflammation in Obesity. \emph{J Dent Res.} 2024;103(12):1313-1322.
#' doi:10.1177/00220345241280743
#'
#' @examples
#' data(ExampleData3)
"ExampleData3"

#' Example Cytokine Profiling Data 4.
#'
#' Contains observed concentrations of cytokines and their respective treatment
#' and groups, derived from:
#'
#' @format A data frame with 64 rows and 14 columns:
#' \describe{
#'  \item{Group}{Group assigned to the subjects.}
#'  \item{Treatment}{Treatment received by subjects.}
#'  \item{IL-17F}{Observed concentration of IL-17F cytokine.}
#'  \item{GM-CSF}{Observed concentration of GM-CSF cytokine.}
#'  \item{IFN-G}{Observed concentration of IFN-G cytokine.}
#'  \item{IL-10}{Observed concentration of IL-10 cytokine.}
#'  \item{CCL-20}{Observed concentration of CCL-20 cytokine.}
#'  \item{IL-12}{Observed concentration of IL-12 cytokine.}
#'  \item{IL-13}{Observed concentration of IL-13 cytokine.}
#'  \item{IL-17A}{Observed concentration of IL-17A cytokine.}
#'  \item{IL-22}{Observed concentration of IL-22 cytokine.}
#'  \item{IL-9}{Observed concentration of IL-9 cytokine.}
#'  \item{IL-2}{Observed concentration of IL-2 cytokine.}
#'  \item{IL-21}{Observed concentration of IL-21 cytokine.}
#'  \item{IL-4}{Observed concentration of IL-4 cytokine.}
#'  \item{IL-23}{Observed concentration of IL-23 cytokine.}
#'  \item{IL-5}{Observed concentration of IL-5 cytokine.}
#'  \item{IL-6}{Observed concentration of IL-6 cytokine.}
#'  \item{TNF-A}{Observed concentration of TNF-A cytokine.}
#'  \item{TNF-B}{Observed concentration of TNF-B cytokine.}
#'  }
#'
#' @source Example data compiled for cytokine profiling.
#'
#' @references
#' SantaCruz-Calvo, S., Saraswat, S., Kalantar, G. H., Zukowski, E.,
#' Marszalkowski, H., Javidan, A., Gholamrezaeinejad, F., Bharath, L. P.,
#' Kern, P. A., Zhang, X. D., & Nikolajczyk, B. S. (2024).
#' A unique inflammaging profile generated by T cells from people with obesity
#' is metformin resistant. \emph{GeroScience}, 10.1007/s11357-024-01441-4.
#' Advance online publication. https://doi.org/10.1007/s11357-024-01441-4
#'
#' @examples
#' data(ExampleData4)
"ExampleData4"

#' Example Cytokine Profiling Data 5.
#'
#' Contains observed concentrations of cytokines and their respective treatment
#' and groups, derived from:
#'
#' @format A data frame with 297 rows and 29 columns:
#' \describe{
#'   \item{Group}{Group assigned to the subjects.}
#'   \item{Treatment}{Treatment received by subjects.}
#'   \item{Batch}{Batch number corresponding to the sample.}
#'   \item{Time}{Time point of the measurement.}
#'   \item{IL-17F}{Observed concentration of IL-17F cytokine.}
#'   \item{GM-CSF}{Observed concentration of GM-CSF cytokine.}
#'   \item{IFN-G}{Observed concentration of IFN-G cytokine.}
#'   \item{IL-10}{Observed concentration of IL-10 cytokine.}
#'   \item{CCL-20/MIP-3A}{Observed concentration of CCL.20.MIP.3A cytokine.}
#'   \item{IL-12/P70}{Observed concentration of IL-12/P70 cytokine.}
#'   \item{IL-13}{Observed concentration of IL-13 cytokine.}
#'   \item{IL-15}{Observed concentration of IL-15 cytokine.}
#'   \item{IL-17A}{Observed concentration of IL-17A cytokine.}
#'   \item{IL-22}{Observed concentration of IL-22 cytokine.}
#'   \item{IL-9}{Observed concentration of IL-9 cytokine.}
#'   \item{IL-1B}{Observed concentration of IL-1B cytokine.}
#'   \item{IL-33}{Observed concentration of IL-33 cytokine.}
#'   \item{IL-2}{Observed concentration of IL-2 cytokine.}
#'   \item{IL-21}{Observed concentration of IL-21 cytokine.}
#'   \item{IL-4}{Observed concentration of IL-4 cytokine.}
#'   \item{IL-23}{Observed concentration of IL-23 cytokine.}
#'   \item{IL-5}{Observed concentration of IL-5 cytokine.}
#'   \item{IL-6}{Observed concentration of IL-6 cytokine.}
#'   \item{IL-17E/IL-25}{Observed concentration of IL-17E/IL-25 cytokine.}
#'   \item{IL-27}{Observed concentration of IL-27 cytokine.}
#'   \item{IL-31}{Observed concentration of IL-31 cytokine.}
#'   \item{TNF-A}{Observed concentration of TNF-A cytokine.}
#'   \item{TNF-B}{Observed concentration of TNF-B cytokine.}
#'   \item{IL-28A}{Observed concentration of IL-28A cytokine.}
#' }
#' @source Example data compiled for cytokine profiling.
#' @references
#' Pugh GH, Fouladvand S, SantaCruz-Calvo S, Agrawal M, Zhang XD, Chen J,
#' Kern PA, Nikolajczyk BS.
#' T cells dominate peripheral inflammation in a cross-sectional analysis of
#' obesity-associated diabetes. \emph{Obesity (Silver Spring)}. 2022;30(10):
#' 1983–1994. doi:10.1002/oby.23528.
#'
#' @note
#' The ExampleData5 dataset is the same data as ExampleData1 but with a new
#' column "Batch" added to indicate the batch number corresponding to each sample.
#' The "Batch" column was randomly generated to simulate batch effects in the data.
#'
#' @examples
#' data(ExampleData5)
"ExampleData5"