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 1.4.0 Index]