GatingSet-methods: constructors for GatingSet

In flowWorkspace: Infrastructure for representing and interacting with the gated cytometry

Description

construct object from xml workspace file and a list of sampleIDs (not intended to be called by user.)

construct a gatingset with empty trees (just root node)

construct object from existing gating hierarchy(gating template) and flow data

Usage

## S4 method for signature 'character,character'
GatingSet(x, y, guids, includeGates = FALSE,
  sampNloc = "keyword", xmlParserOption, wsType)

## S4 method for signature 'flowSet,ANY'
GatingSet(x)

## S4 method for signature 'GatingHierarchy,character'
GatingSet(x, y, path = ".", ...)

Arguments

x	character or flowSet or GatingHierarchy
y	character ormissing
guids	character vectors to uniquely identify each sample (Sometime FCS file names alone may not be unique)
includeGates	logical whether to parse the gates or just simply extract the flowJo stats
sampNloc	character scalar indicating where to get sampleName(or FCS filename) within xml workspace. It is either from "keyword" or "sampleNode".
xmlParserOption	integer option passed to xmlTreeParse
wsType	character workspace type, can be value of "win", "macII", "vX", "macIII".
path	character specifies the path to the flow data (FCS files)
...	other arguments. see parseWorkspace

Examples

## Not run: 
#fdata could be a flowSet or ncdfFlowSet
gs <- GatingSet(fdata)

## End(Not run)

flowWorkspace documentation built on July 17, 2017, 2 a.m.

Class '"GatingSetList"'

flowWorkspace index

Retrieve the compensation matrices from a GatingHierarchy