PercentPos.FCS {rflowcyt} | R Documentation

## Calculate the Percent Positive given a percentile

### Description

From a sample of observations, the percentile for a given percent is computed as the value in which there is a given percent of observations that are lower than it. Using `percentile.FCS` will obtain the percentile of interest in a given vector of values.

Given a sample of observed values, the percent positive over a certain percentile value will be calculated and output by using `PercentPos.FCS`.

### Usage

    percentile.FCS(x.vector, percent = 0.999)

    PercentPos.FCS(st.data, percentile)

### Arguments

`x.vector` | numerical vector of observations usually from the control data
`percent` | numeric; the percent at which to obtain the percentile
`st.data` | numerical vector of observations; usually of the cytokine response of the stimulated sample
`percentile` | numerical value of the threshold; usually the 99.9th percentile of the corresponding unstimulated/control sample

### Details

Specifically `percentile.FCS` is used to obtain the percentiles for `PercentPos.FCS` and `ROC.FCS` in the analysis of the upper tail distributions of the stimulated and controls samples of cytokine responses, especially of the Interferon Gamma variable, among HIV positive and HIV negative individuals. This function and analysis can be applied to different scenerios as well.

Usually the Interferon Gamma variable from the FCS object (after gating and subsequent subsets (See `createGate` and `extractGatedData`)), is of interest. The percentile is obtained from the unstimulated or control sample and 100* Percent positives among the cells/observations of the stimulated sample is obtained based on the 99.9th percentile of the control sample. There are differences in the tails of these distributions (stimulated versus control) between HIV positive and HIV negative samples that might better distinguish HIV positive and HIV negative samples. This method was proposed by Zoe Moodie.

### Value

For `percentile.FCS`:
the percentile is returned; the percentile is defined as the numeric value of the observation at the which there is a given percent of observations below this value; the value's label or name is the position of the value in the input vector 'controldata'
For `PercentPos.FCS`:

`percent.pos` | the fraction of the observations above or equal to the threshold/percentile
`total.num` | total number of observations in the sample

### Note

Please note that Percentage Positive = 100 * (percent positive).

### Author(s)

A.J. Rossini and J.Y. Wan

### References

Zoe Moodie and Mario Roederer

### See Also

data 'PerPosROC' in rfcdorig package, `ROC.FCS`

### Examples

    if (require(rfcdmin)){

    data.there<-is.element(c("st.1829", "unst.1829", "unst.DRT", "st.DRT"),objects())
    if ( ( sum(data.there) != length(data.there) )){
    ## obtaining the FCS objects from VRC data
    data(VRCmin)
    }
    #hiv negative one individual, 1829
    #stimulated sample
    INFg.st.neg<-st.1829@data[,4]
    #control sample
    INFg.unst.neg<-unst.1829@data[,4]

    #hiv positive one individual, DRT
    #stimulated sample
    INFg.st.pos<-st.DRT@data[,4]
    #control sample
    INFg.unst.pos<-unst.DRT@data[,4]

    c.neg<-percentile.FCS(INFg.unst.neg)
    c.pos<-percentile.FCS(INFg.unst.pos)

    #percent positive for two individuals
    p.neg<-PercentPos.FCS(INFg.st.neg, c.neg)
    p.pos<-PercentPos.FCS(INFg.st.pos, c.pos)

    ### percentage positive
    ptg.neg<-100*p.neg$percent.pos
    ptg.pos<-100*p.pos$percent.pos
    }

[Package rflowcyt version 1.16.0 Index]