Automated gating of single populations in 2D

Description

This function tries to fit a single norm2Filter based on a rough preselection of the data. This function is considered internal. Please use the API provided by lymphGate.

Usage

autoGate(x, ..., scale = 2.5)

Arguments

Details

The flowSet is first filtered using a rectangleGate and the norm2Filter is subsequently fitted to the remaining subset.

Value

A list with items:

Author(s)

Florian Hahne

See Also

lymphGate, norm2Filter

Examples

data(GvHD)
flowStats:::autoGate(GvHD[10:15], "FSC-H"=c(100,500), "SSC-H"=c(0, 400))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(flowStats)
Loading required package: flowCore
Loading required package: fda
Loading required package: splines
Loading required package: Matrix

Attaching package: 'Matrix'

The following object is masked from 'package:flowCore':

    %&%


Attaching package: 'fda'

The following object is masked from 'package:graphics':

    matplot

Loading required package: mvoutlier
Loading required package: sgeostat
sROC 0.1-2 loaded
Loading required package: cluster
Loading required package: flowWorkspace
Loading required package: flowViz
Loading required package: lattice
Loading required package: ncdfFlow
Loading required package: RcppArmadillo
Loading required package: BH
Loading required package: gridExtra
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/flowStats/autoGate.Rd_%03d_medium.png", width=480, height=480)
> ### Name: autoGate
> ### Title: Automated gating of single populations in 2D
> ### Aliases: autoGate
> ### Keywords: misc
> 
> ### ** Examples
> 
> 
> data(GvHD)
> flowStats:::autoGate(GvHD[10:15], "FSC-H"=c(100,500), "SSC-H"=c(0, 400))
$x
A flowSet with 6 experiments.

An object of class 'AnnotatedDataFrame'
  rowNames: s6a03 s6a04 ... s7a01 (6 total)
  varLabels: Patient Visit ... name (5 total)
  varMetadata: labelDescription

  column names:
  FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time

$n2gate
norm2Filter 'defaultNorm2Filter' in dimensions FSC-H and SSC-H with parameters:
  method: covMcd 
  scale.factor: 2.5 
  n: 50000 


$n2gateResults
A list of filterResults for a flowSet containing 6 frames
produced by the filter named 'defaultNorm2Filter'

> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>