GateFinder-package {GateFinder} | R Documentation

## GateFinder

### Description

Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.

### Details

Package: | GateFinder
Type: | Package
Version: | 1.0
Date: | 2013-12-21
License: | Artistic-2.0

~~ An overview of how to use the package, including the most important ~~ ~~ functions ~~

### Author(s)

Nima Aghaeepour <naghaeep@gmail.com> and Erin F. Simonds <erin.simonds@gmail.com>

### Examples

    library(flowCore)

    data(LPSData)
    ##Select the target population. In this case cells with those with a pP38 expression (dimension 34) of higher than 3.5.
    targetpop <- (exprs(rawdata)[,34]>3.5)

    ##Subset the markers that should be considered for gating.
    x=exprs(rawdata)[,prop.markers]
    colnames(x)=marker.names[prop.markers]

    ##Run GateFinder.
    ans=GateFinder(x, targetpop)

    ##Make the plots.
    plot (x, ans, c(2,3), targetpop)
    plot(ans)

    ##Alternatively, using a flowFrame:
    x=new('flowFrame', exprs=x)
    ans=GateFinder(x, targetpop)

    ##Now you can use the gates and filters to subset the flowFrame. E.g.:
    split(x, ans@flowEnv$Filter2)

    ##This function relies on an EXPERIMENTAL feature in flowUtils. Please be cautious when replying on this.
    ##Don't run without the optional flowUtils package installed.
    ##To write the gates into a GatingML file:
    ##library(flowUtils)
    ##write.gatingML(ans@flowEnv, 'GatingML.xml')

[Package GateFinder version 1.8.0 Index]