R/hdacTR_smallExample.R

In TPP: Analyze thermal proteome profiling (TPP) experiments

#' @title Example subset of a Panobinostat TPP-TR dataset and the
#'   corresponding configuration table to start the analysis.
#' @name hdacTR_smallExample
#' @docType data
#' @description Example dataset obtained by TPP-TR experiments for analysis by 
#' the TPP-package. It contains all necessary arguments to start the analysis
#' (config table and list of data frames).
#' @seealso \code{\link{hdacTR_data}}, \code{\link{hdacTR_config}}
#' @references Franken, H, Mathieson, T, Childs, D. Sweetman, G. Werner, T. Huber, W. & Savitski, M. M. (2015),
#'   Thermal proteome profiling for unbiased identification of drug targets and detection of downstream effectors.
#'   Nature protocols 10(10), 1567-1593.
NULL
#' 
#' @rdname hdacTR_data
#' @name hdacTR_data
#' @title TPP-TR example dataset.
#' @description Example subset of a dataset obtained by TPP-TR experiments to 
#'   investigate possible targets for HDAC inhibitor Panobinostat.
#' @details \code{hdacTR_data} is a list of data frames that contain
#'   measurements for HDACs as well as a random selection of 500 further
#'   proteins.
#'   
#'   You can use this dataset to explore the \code{\link{TPP}} package 
#'   functionalities without invoking the whole time consuming analysis on the 
#'   whole dataset.
#'   
#'   The original dataset is located in the folder 
#'   \code{'example_data/TR_example_data'} in the package's installation
#'   directory. You can find it on your system by the \code{R} command
#'   \code{system.file('example_data', package = 'TPP')}.
#'   
#'   The measurements were generated by four separate multiplexed TMT 
#'   experiments with 10 TMT labels each.
#'   Quantitative values per protein were obtained by the python  
#'   software isobarQuant and converted to fold changes relative to the lowest 
#'   temperature.
#'   The raw data before quantification can be found in the \code{proteomicsDB}
#'   database (http://www.proteomicsdb.org/#projects/4221/3101) with the following sample mapping:
#'   
#'   \itemize{ 
#'   \item{\code{Panobinostat_1}: }{MS-experiment numbers P85192B02-B10} 
#'   \item{\code{Panobinostat_2}: }{MS-experiment numbers P85881B02-B10} 
#'   \item{\code{Vehicle_1}: }{MS-experiment numbers P85202B02-B10} 
#'   \item{\code{Vehicle_2}: }{MS-experiment numbers P85891B02-B10} 
#'   }
#'   
#' @seealso \code{\link{hdacTR_smallExample}}, \code{\link{hdacTR_config}}
#' @references Franken, H, Mathieson, T, Childs, D. Sweetman, G. Werner, T. Huber, W. & Savitski, M. M. (2015),
#'   Thermal proteome profiling for unbiased identification of drug targets and detection of downstream effectors.
#'   Nature protocols 10(10), 1567-1593.
NULL

#'
#'@rdname hdacTR_config
#'@name hdacTR_config
#'@title The configuration table to analyze \link{hdacTR_data}.
#'@description The configuration table to analyze \link{hdacTR_data}.
#'@details \code{hdacTR_config} is a data frame that specifies the experiment 
#'  name, isobaric labels, and the administered temperatures at each 
#'  label.
#' @seealso \code{\link{hdacTR_smallExample}}, \code{\link{hdacTR_data}}
#' @references Franken, H, Mathieson, T, Childs, D. Sweetman, G. Werner, T. Huber, W. & Savitski, M. M. (2015),
#'   Thermal proteome profiling for unbiased identification of drug targets and detection of downstream effectors.
#'   Nature protocols 10(10), 1567-1593.
NULL