runflowcytests {rflowcyt} | R Documentation

## Tests the equivalence of two univariate sample distributions by using four different methods

### Description

Runs the following flowcytests:

1. `WLR.flowcytest`
  weighted log rank test (by default when rho=0) and a the plot of survival curves for both samples is also output
2. `KS.flowcytest`
  Kolmogorov-Smirnoff test for the difference in distributions for the control and the stimulated
3. `ProbBin.flowcytest`
  Statistics proposed by Keith A. Baggerly and Mario Roederer which include Chi-squared and Normal tests for the PB metric via probability binning (both based on the control data only ("by.control") and based on the combined dataset of both the stimulated and the control samples ("combined")
4. `pkci2.flowcytest`
  Tests the difference of the upper tails of the two distributions

### Usage

    runflowcytests(controldata, stimuldata, flowcytests = c("WLR", "KS",
                     "ProbBin.by.control", "ProbBin.combined", "pkci2"),
                     N.in.bin = 100, varname = "", title = " ", output.all
                     = FALSE, graph.outlay = c(3, 2), crit.pkci2 = 0.999,
                     alpha.pkci2 = 0.05, na.action.WLR =
                     options()$na.action, rho.WLR = 0, WLR.plotted=TRUE, alternative.KS =
                     "two.sided", ..., KS.plotted=TRUE,
                               PBobj.plotted=TRUE,
                    PBobj.plots.made=c("both", "stimulated", "unstimulated"))

### Arguments

`controldata` | a vector of values/fluoroescent measurements; a univariate control sample
`stimuldata` | a vector of values/fluoroescent measurements; a univariate stimulated sample
`flowcytests` | vector denoting the names of the tests that are implemented; default is a vector of all the test names
`N.in.bin` | a number which denotes the number per bin in used in probability binning
`varname` | character strong of the name of the variable under investigation (this is usually the gamma interferon variable)
`title` | character string of the title of the plots
`output.all` | boolean; if TRUE then all the statistics and p-values obtained are output in list form by test; if FALSE then only the names of the statistics, the statistics, the names of the p-values and the p-values are output in a data.frame; default is FALSE.
`graph.outlay` | a vector of length 2, describing the number of graphs on each row and the number of graphs on each column, respectively
`crit.pkci2` | the percent of control sample to above the meaningful percentile (usually 99.9th percentile) (for pkci2.flowcytest)
`alpha.pkci2` | Type I error rate for construction of the (1-alpha)% Confidence Interval (for pkci2.flowcytest)
`na.action.WLR` | a missing-data filter function. This is applied to the `model.frame` after any subset argument has been used. Default is `options()\$na.action` (as quoted from the `survdiff` documentation)
`rho.WLR` | the exponent in $S(t)^rho$, where S is the Kaplan-Meier estimate of survival; A value of 0 specifies using the weighted log-rank test, and a value of 1 specifies using the Peto and Peto modification of the Gehan-Wilcoxon test.
`WLR.plotted` | boolean; if TRUE, then plot is made; otherwise if FALSE, plotting is surpressed; default=TRUE
`alternative.KS` | character string of the alternative hypothesis: "two-sided" Two sided alternative hypoothesis "less" One-sided alternative hypothesis: controldata distribution is less than the stimuldata distribution "greater" One-sided alternative hypothesis: controldata distribution is greater than the stimuldata distribution
`...` | other options in `KS.flowcytest`
`KS.plotted` | boolean to display the corresponding plot; default is TRUE and the plot will be displayed
`PBobj.plotted` | boolean; if TRUE then histograms of the ProbBin.FCS object will be plotted; if FALSE, then these plots are surpressed; default is TRUE
`PBobj.plots.made` | character string denoting which histogram plot should be displayed; default is "both"

### Value

A dataframe consisting of 4 columns and 20 rows. The labels on the columns are "statistics.names", "statistics", "pvalues.names", and "pvalues" or if 'output.all' is TRUE, a list of statistics and tesing output by test name will be produced. Also 6 to 0 plots are produced.

### WARNING

Usually the FCS object is gated and subset prior to this testing and analysis. Also this function requires the library `survival`.

### Note

For more information about the output, please see the other flowcytests in the "See Also" Section.

### Author(s)

Zoe Moodie, A.J. Rossini, J.Y. Wan

### References

Keith A. Baggerly "Probability Binning and Test Agreement between Multivariate Immunofluorescence Histograms: Extending the Chi-Squared test" Cytometry 45: 141:150 (2001).

Harrington, D. P. and Fleming, T. R. (1982). "A class of rank test procedures for censored survival data". Biometrika 69, 553-566.

Zoe Moodie, PhD Statistical Center for HIV/AIDS Research and Prevention (SCHARP) Fred Hutchison Cancer Research Center Seattle, WA 98109-1024

Mario Roederer, et al. "Probability Binning Comparison: A Metric for Quantitating Univariate Distribution Differences" Cytometry 45:37-46 (2001).

### See Also

`pkci2.flowcytest`, `ProbBin.flowcytest`, `KS.flowcytest`, `WLR.flowcytest`

### Examples

    if (require(rfcdmin)){
    ## obtaining the FCS objects from VRC data
    if ( !(is.element("unst.1829", objects()) & is.element("st.1829",
    objects()) & is.element("unst.DRT", objects()) & is.element("st.DRT",
    objects())) ){
    data(VRCmin)
    }

    ## This only serves as an example.  Usually the FCS object is
    ## gated and then subset

    ## HIV negative individual 1829
      IFN.control<-unst.1829@data[1:2000,4]
      IFN.stimul<-st.1829@data[1:2000,4]

    if (interactive()){

    ## running all the tests
    output1.runall<-runflowcytests(IFN.control, IFN.stimul,
    varname="Interferon Gamma",
    title="HIV negative individual 1829", crit.pkci2=0.9999)
    }

    ## HIV positive individual DRT
      IFN.control2<-unst.DRT@data[1:2000,4]
      IFN.stimul2<-st.DRT@data[1:2000,4]

    if (interactive()){
    ## running only WLR.flowcytest and pkci2.flowcytest
    output2.runall<-runflowcytests(IFN.control2, IFN.stimul2,
    flowcytests=c("WLR","pkci2"), varname="Interferon Gamma",
    title="HIV negative individual 1829", crit.pkci2=0.9999)
    }
    ## This is an artifical example, but one would expect the
    ## distributions of the stimulated and control samples
    ## to be the same in the HIV negative individual 1829
    ## and to be different in the HIV positive individual DRT
    ## The test in this example is a bit contrived but
    ## the bigger picture is achieved.
    }

[Package rflowcyt version 1.12.0 Index]