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flowWorkspace (version 3.12.06)

Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore

Description

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

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Version

Version

3.12.06

License

Artistic-2.0

Maintainer

Greg Finak

Last Published

February 15th, 2017

Functions in flowWorkspace (3.12.06)

flowWorkspace-package

Import and replicate flowJo workspaces and gating schemes using flowCore.

flowWorkspace.par.set

flowWorkspace.par.set sets a set of parameters in the flowWorkspace package namespace.

GatingSet-class

Class "GatingSet"

getParent,GatingSet,character-method

Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy

GatingSet,character,character-method

constructors for GatingSet

getProp,GatingHierarchy,character-method

Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy

plotPopCV,GatingHierarchy-method

Plot the coefficient of variation between flowJo and flowCore population statistics for each population in a gating hierarchy.

Determine tick mark locations and labels for a given channel axis

setNode,GatingHierarchy,character,character-method

Update the name of one node in a gating hierarchy/GatingSet.

subset.GatingSet

subset the GatingSet/GatingSetList based on 'pData'

GatingSetList-class

Class "GatingSetList"

getCompensationMatrices,GatingHierarchy-method

Retrieve the compensation matrices from a GatingHierarchy

getTransformations,GatingHierarchy-method

Return a list of transformations or a transformation in a GatingHierarchy

insert a dummy gate to the GatingSet

sampleNames,GatingHierarchy-method

Get/update sample names in a GatingSet

transform,GatingSet-method

tranform the flow data asssociated with the GatingSet

recompute,GatingSet-method

Compute the cell events by the gates stored within the gating tree

filterObject,rectangleGate-method

convert flowCore filter to a list

flowData,GatingSet-method

Fetch or replace the flowData object associated with a GatingSet .

getGate,GatingHierarchy,character-method

Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.

Return the single-cell matrix of 1/0 dichotomized expression

getKeywords,flowJoWorkspace,character-method

getNodes,GatingSet-method

Get the names of all nodes from a gating hierarchy.

parseWorkspace,flowJoWorkspace-method

Parse a flowJo Workspace

determine the flow data associated with a Gating Hiearchy is based on `ncdfFlowSet` or `flowSet`

keyword,GatingHierarchy,character-method

Retrieve a specific keyword for a specific sample in a GatingHierarchy or or set of samples in a GatingSet or GatingSetList

pData,GatingHierarchy-method

read/set pData of flow data associated with GatingSet or GatingSetList

add,GatingSet,list-method

Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.

getFJWSubsetIndices

Fetch the indices for a subset of samples in a flowJo workspace, based on a keyword value pair

getData,GatingHierarchy,missing-method

get gated flow data from a GatingHierarchy/GatingSet/GatingSetList

archive/unarchive to/from a tar file

getSamples,flowJoWorkspace-method

Get a list of samples from a flowJo workspace

getSingleCellExpression,GatingSet,character-method

Return the cell events data that express in any of the single populations defined in y

get/set the log level

make a formula from a character vector

setGate,GatingHierarchy,character,filter-method

update the gate

save/load a GatingSet/GatingSetList to/from disk.

construct the flowJo-type biexponentioal transformation function

flowJoWorkspace-class

An R representation of a flowJo workspace.

flowWorkspace.par.init

workspace version is parsed from xml node '/Workspace/version' in flowJo workspace and matched with this list to dispatch to the one of the three workspace parsers

GatingHierarchy-class

Class GatingHierarchy

getIndices,GatingSet,name-method

routine to return the indices by specify boolean combination of reference nodes:

getIndices,GatingHierarchy,character-method

Get the membership indices for each event with respect to a particular gate in a GatingHierarchy

lapply,GatingSet-method

apply FUN to each sample (i.e. GatingHierarchy)

length,GatingSet-method

Methods to get the length of a GatingSet

plot,GatingSet,missing-method

plot a gating tree

Plot gates and associated cell population contained in a GatingHierarchy or GatingSet

booleanFilter-class

A class describing logical operation (& or |) of the reference populations

clone a GatingSet

getSample,GatingHierarchy-method

Get the sample name associated with a GatingHierarchy

getSampleGroups,flowJoWorkspace-method

Get a table of sample groups from a flowJo workspace

Fetch the flowData object associated with a GatingSet .

openWorkspace,character-method

Open/Close a flowJo workspace