flowPloidy {flowPloidy} | R Documentation

## flowPloidy: A package for analyzing Flow Cytometry Histograms

### Description

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.

### Details

Please see the vignettes for an overview: `histogram-tour` and `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.

### Primary Functions

Most users will need only the functions:

1. `viewFlowChannels`, to determine the name of the primary data channel to use.

2. `batchFlowHist`, to load a list of FCM files into R.

3. `browseFlowHist`, to review and correct the model-fitting for the files, using an interactive graphical browser.

4. `tabulateFlowHist`, to extract the results and save them to a file.

### Additional User Tools

Additional functions for inspecting and manipulating `FlowHist` objects and analyses:

1. `FlowHist`, to load a single FCM file into R.

2. `plot.FlowHist`, for plotting the data and fitted model using base R graphics.

3. `pickInit`, to interactively select initial peak estimates, using base R graphics (this is more easily accomplished via `browseFlowHist`.

4. `setBins`, to reset the bins, selecting the number of bins to use.

5. `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.

6. `updateFlowHist`, to update the settings for an FCM file.

### 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:

1. `fhAccessors`, for inspecting the slots of a `FlowHist` object

2. `findPeaks`, the functions which perform the initial peak detection

3. `ModelComponent`, the S4 class for the various model components used in constructing the non-linear regression model.

4. `GaussianComponents`, a description of the Gaussian model component that is fit to cell peaks.

5. `DebrisModels`, a description of the debris model components.

6. `FlowStandards`, the S4 class for the size standard data.

7. `plotFH`, a low-level plotting function for displaying raw histogram data.

8. `resetFlowHist`, a function for safely resetting various portions of a `FlowHist` object.

9. `flowModels`, functions for assembling `ModelComponent` into a complete model.

10. `fhDoNLS`, `fhDoCounts`, `fhDoCV`, `fhDoRCS`: the functions which actually complete the model fitting and extract the parameters of interest.

11. `setGate`, the function for applying a gate to a `FlowHist` object.

### Author(s)

Tyler Smith

[Package flowPloidy version 1.18.0 Index]