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:
flowPloidy-gettingStarted. To follow along with the examples in
the vignettes, and also in the documentation listed below, you'll need
to install the
flowPloidyData package from Bioconductor.
Most users will need only the functions:
viewFlowChannels, to determine the name of the
primary data channel to use.
batchFlowHist, to load a list of FCM files into R.
browseFlowHist, to review and correct the
model-fitting for the files, using an interactive graphical browser.
tabulateFlowHist, to extract the results and save
them to a file.
Additional functions for inspecting and manipulating
FlowHist objects and analyses:
FlowHist, to load a single FCM file into R.
plot.FlowHist, for plotting the data and fitted
model using base R graphics.
pickInit, to interactively select initial peak
estimates, using base R graphics (this is more easily accomplished via
setBins, to reset the bins, selecting the number of
bins to use.
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.
updateFlowHist, to update the settings for an FCM
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:
fhAccessors, for inspecting the slots of a
findPeaks, the functions which perform the initial
ModelComponent, the S4 class for the various model
components used in constructing the non-linear regression model.
GaussianComponents, a description of the Gaussian
model component that is fit to cell peaks.
DebrisModels, a description of the debris
FlowStandards, the S4 class for the size standard
plotFH, a low-level plotting function for displaying
raw histogram data.
resetFlowHist, a function for safely resetting
various portions of a
flowModels, functions for assembling
ModelComponent into a complete model.
fhDoRCS: the functions which
actually complete the model fitting and extract the parameters of
setGate, the function for applying a gate to a
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