R/flowPloidy.R

In flowPloidy: Analyze flow cytometer data to determine sample ploidy

#' flowPloidy: A package for analyzing Flow Cytometry Histograms
#'
#' The flowPloidy package provides functions for reading and analyzing flow
#' cytometry histograms. Specifically, it builds and fits a non-linear
#' regression model, from which peak parameters (mean, CV) can be
#' estimated. In normal use, samples will include a co-chopped size
#' standard. Comparing the unknown peak mean to the standard peak mean, we
#' determine the genome content for the unknown sample.
#'
#' Please see the vignettes for an overview: \code{histogram-tour} and
#' \code{flowPloidy-gettingStarted}. To follow along with the examples in
#' the vignettes, and also in the documentation listed below, you'll need
#' to install the \code{flowPloidyData} package from Bioconductor.
#' 
#' @section Primary Functions:
#'
#' Most users will need only the functions:
#'
#' \enumerate{
#' \item \code{\link{viewFlowChannels}}, to determine the name of the
#'   primary data channel to use.
#' \item \code{\link{batchFlowHist}}, to load a list of FCM files into R.
#' \item \code{\link{browseFlowHist}}, to review and correct the
#'   model-fitting for the files, using an interactive graphical browser.
#' \item \code{\link{tabulateFlowHist}}, to extract the results and save
#'   them to a file.
#' }
#'
#' @section Additional User Tools:
#' 
#' Additional functions for inspecting and manipulating
#' \code{\link{FlowHist}} objects and analyses:
#'
#' \enumerate{
#' \item \code{\link{FlowHist}}, to load a single FCM file into R.
#' \item \code{\link{plot.FlowHist}}, for plotting the data and fitted
#'   model using base R graphics.
#' \item \code{\link{pickInit}}, to interactively select initial peak
#'   estimates, using base R graphics (this is more easily accomplished via
#'   \code{\link{browseFlowHist}}.
#' \item \code{\link{setBins}}, to reset the bins, selecting the number of
#'   bins to use.
#' \item \code{\link{fhAnalyze}}, to (re-)analyze the FCM data, presumably
#'   after updating the settings for a file. Most functions that make
#'   changes that would require reanalysis provide the option to do this
#'   automatically, and this option is usually the default.
#' \item \code{\link{updateFlowHist}}, to update the settings for an FCM
#'   file.
#' }
#'
#' @section Internal Functions:
#'
#' These functions aren't necessary for regular use, and are not exported
#' for direct access by users. They may be useful to those interested in
#' modifying or extending the package, or just curious about details:
#'
#' \enumerate{
#' \item \code{\link{fhAccessors}}, for inspecting the slots of a
#'   \code{\link{FlowHist}} object 
#' \item \code{\link{findPeaks}}, the functions which perform the initial
#'   peak detection
#' \item \code{\link{ModelComponent}}, the S4 class for the various model
#'   components used in constructing the non-linear regression model.
#' \item \code{\link{GaussianComponents}}, a description of the Gaussian
#'   model component that is fit to cell peaks.
#' \item \code{\link{DebrisModels}}, a description of the debris
#'   model components.
#' \item \code{\link{FlowStandards}}, the S4 class for the size standard
#'   data. 
#' \item \code{\link{plotFH}}, a low-level plotting function for displaying
#'   raw histogram data.
#' \item \code{\link{resetFlowHist}}, a function for safely resetting
#'   various portions of a \code{\link{FlowHist}} object.
#' \item \code{\link{flowModels}}, functions for assembling
#'   \code{\link{ModelComponent}} into a complete model.
#' \item \code{\link{fhDoNLS}}, \code{\link{fhDoCounts}},
#'   \code{\link{fhDoCV}}, \code{\link{fhDoRCS}}: the functions which
#'   actually complete the model fitting and extract the parameters of
#'   interest.
#' \item \code{\link{setGate}}, the function for applying a gate to a
#'   \code{\link{FlowHist}} object.
#' }
#'
#'
#' @author Tyler Smith
#' @docType package
#' @name flowPloidy
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