WLR.flowcytest {rflowcyt} | R Documentation

## Weighted Logrank Test for testing the differences between time-to-event, survival curves

### Description

Using a survival method developed by Flemming and Harrington, this function examines the difference in the survival curves of two samples in order to determine a distribution difference between the two samples. A plot of the two super-imposed survival curves is displayed.

### Usage

    WLR.flowcytest(controldata, stimuldata, title = "", varname = "",
                   na.action.WLR = options()$na.action, rho.test = 0,
                   WLR.plotted=TRUE, MY.DEBUG=TRUE)

### Arguments

`controldata` | numerical vector of observations of the control data for one variable
`stimuldata` | numerical vector of observations of the stimulated data for the same variable as the control
`title` | character string describing the title
`varname` | character string describing the name of the variable
`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 from the survival package.)
`rho.test` | the exponent, rho in S(t)^rho, where S is the Kaplan-Meier estimate of survival; A rho value of 0 specifies using the weighted log-rank test, and a value of 1 specifies using the Peto & Peto modification of the Gehan-Wilcoxon test.
`WLR.plotted` | boolean; if TRUE, then plot is made; otherwise if FALSE, plotting is surpressed; default=TRUE
`MY.DEBUG` | boolean; if TRUE, the test is printed out with comments; if FALSE then these comments are surpressed

### Details

The null hypothesis is that the two survival curves are the same in both samples. If there is a significant difference then a large chi-squared one statistic corresponding to a small p-value (usually < 0.05, where the Type I error rate=alpha=0.05) will suggest this significance.

This function uses 'survdiff' in the survival package. The following is a direct quote from the 'survdiff' documentation: "This function (survdiff) implements the G-rho family of Harrington and Fleming (1982), with weights on each death of S(t)^rho, where S is the Kaplan-Meier estimate of survival.With `rho = 0' this is the log-rank or Mantel-Haenszel test, and with `rho = 1' it is equivalent to the Peto & Peto modification of the Gehan-Wilcoxon test."

In this flowcytometry analysis, we are not dealing with the proportion of survival, persay, but instead in terms of the proportion of observations/cells beyond a certain value of the interferon gamma variable.

### Value

`p.val.1sid.chisq.WLR` | p-value associated with a chi-squared statistic with one degree of freedom
`chisq.WLR` | the chi-squared statistic in the test of the difference in survival curves
`n.WLR` | a numeric vector of the number of subjects in the control and the stimulated samples, respectively
`obs.WLR` | numeric vector of the weighted observed number of events in each sample, control and stimulated, respectively
`exp.WLR` | numeric vector of the weighted expected number of events in each sample, control and stimulated, respectively
`var.WLR` | the variance matrix of the test (control, stimulated)

A survival plot is also made with the two survival curves, labeled "Control" and "Stimulated" and super-imposed on one plot.

### WARNING

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

### Note

Other flowcytests are available such as `pkci2.flowcytest`, `ProbBin.flowcytest`, `KS.flowcytest`, which test the equivalence of two sample distributions. Generally, comparing the control and stimulated samples of the interferon gamma variable is of interest.

### Author(s)

A.J. Rossini and J.Y. Wan

### References

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

### See Also

`pkci2.flowcytest`, `ProbBin.flowcytest`, `KS.flowcytest`, `runflowcytests`, the function 'survdiff' in the survival package.

### Examples

    if (require(rfcdmin)){

    data.there<-is.element(c("st.1829", "unst.1829", "st.DRT", "unst.DRT"),objects())
    if ( ( sum(data.there) != length(data.there) )){
    ## obtaining the FCS objects from VRC data
    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()==TRUE){
    par(mfrow=c(2,2))
    WLR.flowcytest(IFN.control, IFN.stimul,
    title="HIV negative individual 1829",
    varname="Interferon Gamma")
    }
    ## HIV positive individual DRT
      IFN.control2<-unst.DRT@data[1:2000,4]
      IFN.stimul2<-st.DRT@data[1:2000,4]

    if (interactive()==TRUE){
    WLR.flowcytest(IFN.control2, IFN.stimul2,
    title="HIV positive individual DRT",
    varname="Interferon Gamma")
    }
    ## 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 1.16.0 Index]