R/data.R

In lucyleeow/CellProfileR: Analyse Cell Morphology Data Generated By CellProfiler

#' Raw CellProfiler data
#' 
#' Raw CellProfiler data from imaging cells in a 3 (24 by 16) well plate. 
#' Cells in each well were exposed to a different compound, left to grow and
#' then imaged using three stains; CMFDA, DAPI and Phalloidin. CellProfiler was 
#' then used to extract phenotype data from images taken of each well.
#' 
#' Each row provides metatdata and information extracted by 
#' CellProfiler from one image taken of cells grown in one well. There were
#' four rows (images taken) per well. There were two 384 well plates. Only 100 
#' wells from each 384 well plate were included to minimise the size of the data 
#' set. A number of columns output by CellProfiler were also removed (including 
#' 'Mean' and 'StDev' columns) to minimise the size of the data set.
#' 
#' Details of how the CellProfiler columns were named are as follows:
#' \describe{
#'     \item{MeasurementType}{This tells you the type of data contained in the
#'       measurement, if relevant. This is often 'Median', which means that the 
#'       median value of that measurement, for all cells identified in that 
#'       image, is provided.}
#'     \item{Location}{The location of the cell this measurement is from. This
#'       is generally 'Nuclei', 'Cytoplasm' or 'Actin' (which captures  
#'       cell cytoskeleton details.)}
#'     \item{Category}{Description of the type of measurement taken. For 
#'       example 'AreaShape' provides information about the area or shape of
#'       a cell location and 'Texture' provides texture information about
#'       a cell location.}
#'     \item{SpecificFeatureName}{Details about the measurement made.}
#' }
#' 
#' More details about how each variable (column) is named and how each variable 
#' is calculated can be found in the 
#' \href{http://cellprofiler-manual.s3.amazonaws.com/CellProfiler-3.1.5/index.html}{CellProfiler documentation}.
#' 
#' 
#' @format A dataframe with 800 rows (400 rows per plate), and 218 variables:
#' \describe{
#'     \item{Metadata_Barcode}{Plate ID.}
#'     \item{Metadata_WellID}{Well ID. The plate is numbered such that the 
#'       columns go from 1-24 and the rows from A-P.}
#'     \item{Compound_ID}{The compound ID of the compound the well was exposed
#'       to. "DMSO" was the negative control compound.}
#'     \item{Concentration}{The concentration of the compound the well was
#'       exposed to. Several concentrations of the same compound was used for
#'       some compounds.}
#'     \item{CellProfiler output}{The remaining columns were output by 
#'       CellProfiler. Phenotype columns from CellProfiler have the general 
#'       structure: `MeasurementType_Location_Category_SpecificFeatureName` and
#'       are described in more detail below.}
#' }   
#'       
#' 
#' 
#' 
"CPdata"