flowFP: Fingerprinting for Flow Cytometry

Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("flowFP")
AuthorHerb Holyst <holyst@mail.med.upenn.edu>, Wade Rogers <rogersw@mail.med.upenn.edu>
Bioconductor views CellBasedAssays Clustering FlowCytometry Visualization
Date of publicationNone
MaintainerHerb Holyst <holyst@mail.med.upenn.edu>
LicenseArtistic-2.0
Version1.34.0

View on Bioconductor

Man pages

append-methods: Methods to append flowFP fingerprints to a flowFPPlex

binBoundary-methods: Return bin boundaries for a flowFPModel

counts-methods: Method for getting fingerprint data.

flowFP: Fingerprint constructor

flowFP-class: Fingerprint class description.

flowFPModel: Fingerprint model constructor

flowFPModel-class: Fingerprint model class description.

flowFP-package: Package overview

flowFPPlex: Fingerprint collection constructor.

flowFPPlex-class: Fingerprint collection class description.

fs1: Example FCS flowSet

fs2: Example FCS flowSet

hasClasses-methods: Returns TRUE if the flowFP has a class factor for its...

index-methods: Indexing methods for flowFP and flowFPPlex

is.flowFP: Test to see if object is a flowFP

is.flowFPModel: Test to see if object is a flowFPModel

is.flowFPPlex: Test to see if object is a flowFPPlex

length-methods: The number of fingerprints in a flowFPPlex

name-methods: Get Model Name

nFeatures-methods: Returns the number of features in an object.

nInstances-methods: Returns the number of instances in an object.

nRecursions-methods: Methods to set or get nRecursions

parameters-methods: Return the parameters considered for fingerprinting

plate: 96 well plate data.

plot-methods: Methods for visualizing flowFP objects

sampleClasses-methods: Gets/Sets the sample classes for a fingerprint.

sampleNames-methods: Methods to return sample names from a flowFP object.

show-methods: Methods to view flowFP objects

summary-methods: Summerizes a flowFP object.

tags-methods: Returns tags from a flowFP object.

Functions

append,flowFPPlex,flowFP-method Man page
append,flowFPPlex,flowFPPlex-method Man page
append,flowFPPlex,list-method Man page
append-methods Man page
binBoundary Man page
binBoundary,flowFP-method Man page
binBoundary,flowFPModel-method Man page
binBoundary-methods Man page
counts Man page
counts,flowFP-method Man page
counts,flowFPPlex-method Man page
flowFP Man page
[,flowFP,character-method Man page
flowFP-class Man page
flowFPModel Man page
flowFPModel-class Man page
[,flowFP,numeric-method Man page
flowFP-package Man page
flowFPPlex Man page
[,flowFPPlex,ANY-method Man page
[[,flowFPPlex,ANY-method Man page
flowFPPlex-class Man page
[[<-,flowFPPlex,numeric,ANY,flowFP-method Man page
fs1 Man page
fs2 Man page
hasClasses Man page
hasClasses,flowFP-method Man page
hasClasses,flowFPPlex-method Man page
hasClasses-methods Man page
is.flowFP Man page
is.flowFPModel Man page
is.flowFPPlex Man page
length,flowFPPlex-method Man page
length<-,flowFPPlex,numeric-method Man page
length-methods Man page
[-methods Man page
[[-methods Man page
name Man page
name,flowFP-method Man page
name,flowFPModel-method Man page
name,flowFPPlex-method Man page
name-methods Man page
nFeatures Man page
nFeatures,flowFP-method Man page
nFeatures,flowFPModel-method Man page
nFeatures,flowFPPlex-method Man page
nFeatures-methods Man page
nInstances Man page
nInstances,flowFP-method Man page
nInstances,flowFPPlex-method Man page
nInstances-methods Man page
nRecursions Man page
nRecursions<- Man page
nRecursions,flowFP-method Man page
nRecursions,flowFPModel-method Man page
nRecursions<-,flowFPModel,numeric-method Man page
nRecursions<-,flowFP,numeric-method Man page
nRecursions,flowFPPlex-method Man page
nRecursions-methods Man page
parameters,flowFP-method Man page
parameters,flowFPModel-method Man page
parameters-methods Man page
plate Man page
plot,flowFP,flowFrame-method Man page
plot,flowFP,flowSet-method Man page
plot,flowFP,missing-method Man page
plot,flowFPModel,flowFrame-method Man page
plot,flowFPModel,flowSet-method Man page
plot,flowFPModel,missing-method Man page
plot,flowFPPlex,missing-method Man page
plot-methods Man page
sampleClasses Man page
sampleClasses<- Man page
sampleClasses<-,flowFP-method Man page
sampleClasses,flowFP-method Man page
sampleClasses<-,flowFPPlex-method Man page
sampleClasses,flowFPPlex-method Man page
sampleClasses-methods Man page
sampleNames Man page
sampleNames,flowFP-method Man page
sampleNames,flowFPPlex-method Man page
sampleNames-methods Man page
show,flowFP-method Man page
show,flowFPModel-method Man page
show,flowFPPlex-method Man page
show-methods Man page
summary,flowFP-method Man page
summary-methods Man page
tags Man page
tags,flowFP-method Man page
tags-methods Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/AllGenerics.R R/flowFP-utils.R R/flowFP.R R/flowFPModel.R R/flowFPPlex.R R/plot-fancy.R R/plot-grid.R R/plot-model.R R/plot-plate.R R/plot-qc.R R/plot-stack.R R/plot-tangle.R R/plot-utils.R
README
build
build/vignette.rds
cleanup
configure
configure.ac
data
data/datalist
data/fs1.rda
data/fs2.rda
data/plate.rda
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/flowFP_HowTo.R
inst/doc/flowFP_HowTo.Rnw
inst/doc/flowFP_HowTo.pdf
man
man/append-methods.Rd man/binBoundary-methods.Rd man/counts-methods.Rd man/flowFP-class.Rd man/flowFP-package.Rd man/flowFP.Rd man/flowFPModel-class.Rd man/flowFPModel.Rd man/flowFPPlex-class.Rd man/flowFPPlex.Rd man/fs1.Rd man/fs2.Rd man/hasClasses-methods.Rd man/index-methods.Rd man/is.flowFP.Rd man/is.flowFPModel.Rd man/is.flowFPPlex.Rd man/length-methods.Rd man/nFeatures-methods.Rd man/nInstances-methods.Rd man/nRecursions-methods.Rd man/name-methods.Rd man/parameters-methods.Rd man/plate.Rd man/plot-methods.Rd man/sampleClasses-methods.Rd man/sampleNames-methods.Rd man/show-methods.Rd man/summary-methods.Rd man/tags-methods.Rd
src
src/Makevars.in
src/cutest
src/cutest/CuTest.c
src/cutest/CuTest.h
src/cutest/Makefile
src/cutest/README
src/cutest/license.txt
src/cutest/make-tests.sh
src/cutest/test_example.c
src/cutest/test_idx_lut.c
src/cutest/test_median.c
src/cutest/test_variance.c
src/flowFP.c
src/flowFP.h
src/init.c
src/split_utils.c
tests
tests/GNUmakefile
tests/doRUnit.R
tests/unitTests
tests/unitTests/runit.flowFP.R tests/unitTests/runit.flowFPModel.R tests/unitTests/runit.flowFPPlex.R
vignettes
vignettes/flowFP.bib
vignettes/flowFP_HowTo.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.