flowCore: flowCore: Basic structures for flow cytometry data

Provides S4 data structures and basic functions to deal with flow cytometry data.

AuthorB. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan, J. Spidlen, M. Jiang
Date of publicationNone
MaintainerM.Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.40.3

View on Bioconductor

Man pages

actionItem-class: Class "actionItem"

arcsinhTransform: Create the definition of an arcsinh transformation function...

asinht-class: Class "asinht"

asinhtGml2-class: Class asinhtGml2

biexponentialTransform: Compute a transform using the 'biexponential' function

boundaryFilter-class: Class "boundaryFilter"

characterOrTransformation-class: Class "characterOrTransformation"

checkOffset: Fix the offset when its values recorded in header and TEXT...

coerce: Convert an object to another class

compensateActionItem-class: Class "compensateActionItem"

compensatedParameter-class: Class "compensatedParameter"

compensateView-class: Class "compensateView"

compensation-class: Class "compensation"

concreteFilter-class: Class "concreteFilter"

dg1polynomial-class: Class "dg1polynomial"

each_col-methods: Method to apply functions over flowFrame margins

EHtrans-class: Class "EHtrans"

ellipsoidGate: Class "ellipsoidGate"

estimateMedianLogicle: Estimates a common logicle transformation for a flowSet.

exponential-class: Class "exponential"

expressionFilter-class: Class "expressionFilter"

fcReference-class: Class "fcReference" and its subclasses

FCSTransTransform: Computes a transform using the 'iplogicle' function

filter-and-methods: Take the intersection of two filters

filter-class: A class for representing filtering operations to be applied...

filterDetails-methods: Obtain details about a filter operation

filter-in-methods: Filter-specific membership methods

filterList-class: Class "filterList"

filter-methods: Filter FCS files

filter-on-methods: Methods for Function %on% in Package 'flowCore'

filterReference-class: Class filterReference

filterResult-class: Class "filterResult"

filterResultList-class: Class "filterResultList"

filters-class: Class "filters" and "filtersList"

filterSet-class: Class filterSet(deprecated)

filterSummary-class: Class "filterSummary"

filterSummaryList-class: Class "filterSummaryList"

flowCore-package: Provides S4 data structures and basic infrastructure and...

flowFrame-class: 'flowFrame': a class for storing observed quantitative...

flowSet-class: 'flowSet': a class for storing flow cytometry raw data from...

fsApply: Apply a Function over values in a flowSet

gateActionItem-class: Class "gateActionItem"

gateView-class: Class "gateView"

getChannelMarker: get channel and marker information from a 'flowFrame' that...

getIndexSort-methods: Extract Index Sorted Data from an FCS File

GvHD: Extract of a Graft versus Host Disease monitoring experiment...

hyperlog-class: Class "hyperlog"

hyperlogtGml2-class: Class hyperlogtGml2

identifier-methods: Retrieve the GUID of flowCore objects

inverseLogicleTransform: Computes the inverse of the transform defined by the...

invsplitscale-class: Class "invsplitscale"

keyword-methods: Methods to retrieve keywords of a flowFrame

kmeansFilter: Class "kmeansFilter"

linearTransform: Create the definition of a linear transformation function to...

lintGml2-class: Class lintGml2

lnTransform: Create the definition of a ln transformation function...

logarithm-class: Class "logarithm"

logicalFilterResult-class: Class "logicalFilterResult"

logicletGml2-class: Class logicletGml2

logicleTransform: Computes a transform using the 'logicle_transform' function

logtGml2-class: Class logtGml2

logTransform: Create the definition of a log transformation function (base...

manyFilterResult-class: Class "manyFilterResult"

markernames: get or update the marker names

multipleFilterResult-class: Class "multipleFilterResult"

norm2Filter-class: Class "norm2Filter"

normalization-class: Class "normalization"

normalizeActionItem-class: Class "normalizeActionItem"

normalizeView-class: Class "normalizeView"

parameterFilter-class: Class "parameterFilter"

parameters-class: Class "parameters"

parameters-methods: Obtain information about parameters for flow cytometry...

parameterTransform-class: Class "parameterTransform"

polygonGate: Class "polygonGate"

polytopeGate: Define filter boundaries

quadGate: Class "quadGate"

quadratic-class: Class "quadratic"

quadraticTransform: Create the definition of a quadratic transformation function...

randomFilterResult-class: Class "randomFilterResult"

ratio-class: Class "ratio"

ratiotGml2-class: Class "ratiotGml2"

read.FCS: Read an FCS file

read.FCSheader: Read the TEXT section of a FCS file

read.flowSet: Read a set of FCS files

rectangleGate: Class "rectangleGate"

sampleFilter-class: Class "sampleFilter"

scaleTransform: Create the definition of a scale transformation function to...

setOperationFilter-class: Class "setOperationFilter"

singleParameterTransform-class: Class "singleParameterTransform"

sinht-class: Class "sinht"

spillover-flowSet: Compute a spillover matrix from a flowSet

split-methods: Methods to split flowFrames and flowSets according to filters

splitscale-class: Class "splitscale"

splitScaleTransform: Compute the split-scale transformation describe by FL. Battye

squareroot-class: Class "squareroot"

Subset-methods: Subset a flowFrame or a flowSet

subsettingActionItem-class: Class "subsettingActionItem"

subsetting-class: Class "subsetting"

subsettingView-class: Class "subsettingView"

summarizeFilter-methods: Methods for function summarizeFilter

timeFilter-class: Class "timeFilter"

transformActionItem-class: Class "transformActionItem"

transformation-class: Class "transformation"

transform-class: 'transform': a class for transforming flow-cytometry data by...

transformFilter-class: A class for encapsulating a filter to be performed on...

transformList-class: Class "transformList"

transformMap-class: A class for mapping transforms between parameters

transformReference-class: Class "transformReference"

transformView-class: Class "transformView"

truncateTransform: Create the definition of a truncate transformation function...

unitytransform-class: Class "unitytransform"

validFilters: Check if all filters in a filters matches same paramters

view-class: Class "view"

workFlow-class: Class "workFlow"(deprecated)

write.FCS: Write an FCS file

write.flowSet: Write an FCS file

Files in this package

flowCore/DESCRIPTION
flowCore/NAMESPACE
flowCore/R
flowCore/R/AllClasses.R flowCore/R/AllGenerics.R flowCore/R/FCSTransTransform.R flowCore/R/IO.R flowCore/R/RcppExports.R flowCore/R/Rm-methods.R flowCore/R/actionItem-accessors.R flowCore/R/coerce.R flowCore/R/eval-methods.R flowCore/R/fcReference-accessors.R flowCore/R/filterResult-accessors.R flowCore/R/filterResultList-accessors.R flowCore/R/filterSet-accessors.R flowCore/R/filterSummary-accessors.R flowCore/R/flowFrame-accessors.R flowCore/R/flowSet-accessors.R flowCore/R/gatingML.R flowCore/R/identifier-methods.R flowCore/R/in-methods.R flowCore/R/initialize-methods.R flowCore/R/length-methods.R flowCore/R/logicalFilterResult-accessors.R flowCore/R/manyFilterResult-accessors.R flowCore/R/median-logicle-transform.R flowCore/R/multipleFilterResult-accessors.R flowCore/R/names-methods.R flowCore/R/on-methods.R flowCore/R/parameters-methods.R flowCore/R/rectangleGate-accessors.R flowCore/R/show-methods.R flowCore/R/split-methods.R flowCore/R/summarizeFilter-methods.R flowCore/R/summary-methods.R flowCore/R/transformList-accessors.R flowCore/R/utils.R flowCore/R/view-accessors.R flowCore/R/workFlow-accessors.R
flowCore/README.md
flowCore/build
flowCore/build/vignette.rds
flowCore/data
flowCore/data/GvHD.rda
flowCore/data/datalist
flowCore/examples
flowCore/examples/example1.r
flowCore/examples/example2.R
flowCore/hyperlog.notice.html
flowCore/inst
flowCore/inst/NEWS
flowCore/inst/doc
flowCore/inst/doc/HowTo-flowCore.R
flowCore/inst/doc/HowTo-flowCore.Rnw
flowCore/inst/doc/HowTo-flowCore.pdf
flowCore/inst/extdata
flowCore/inst/extdata/0877408774.B08
flowCore/inst/extdata/0877408774.E07
flowCore/inst/extdata/0877408774.F06
flowCore/inst/extdata/compdata
flowCore/inst/extdata/compdata/compmatrix
flowCore/inst/extdata/compdata/data
flowCore/inst/extdata/compdata/data/060909.001
flowCore/inst/extdata/compdata/data/060909.002
flowCore/inst/extdata/compdata/data/060909.003
flowCore/inst/extdata/compdata/data/060909.004
flowCore/inst/extdata/compdata/data/060909.005
flowCore/inst/scripts
flowCore/inst/scripts/smoothScatter
flowCore/inst/scripts/smoothScatter/backcol.jpg
flowCore/inst/scripts/smoothScatter/backgray.jpg
flowCore/inst/scripts/smoothScatter/backhue.jpg
flowCore/inst/scripts/smoothScatter/backsat.jpg
flowCore/inst/scripts/smoothScatter/backval.jpg
flowCore/inst/scripts/smoothScatter/blendFuns.R
flowCore/inst/scripts/smoothScatter/examples.R
flowCore/inst/scripts/smoothScatter/foreground.jpg
flowCore/inst/scripts/smoothScatter/smoothScatterMult.R
flowCore/inst/scripts/smoothScatter/testBlendEBImage.R
flowCore/inst/tests
flowCore/inst/unitTests
flowCore/man
flowCore/man/EHtrans-class.Rd flowCore/man/FCSTransTransform.Rd flowCore/man/GvHD.Rd flowCore/man/Subset-methods.Rd flowCore/man/actionItem-class.Rd flowCore/man/arcsinhTransform.Rd flowCore/man/asinht-class.Rd flowCore/man/asinhtGml2-class.Rd flowCore/man/biexponentialTransform.Rd flowCore/man/boundaryFilter-class.Rd flowCore/man/characterOrTransformation-class.Rd flowCore/man/checkOffset.Rd flowCore/man/coerce.Rd flowCore/man/compensateActionItem-class.Rd flowCore/man/compensateView-class.Rd flowCore/man/compensatedParameter-class.Rd flowCore/man/compensation-class.Rd flowCore/man/concreteFilter-class.Rd flowCore/man/dg1polynomial-class.Rd flowCore/man/each_col-methods.Rd flowCore/man/ellipsoidGate.Rd flowCore/man/estimateMedianLogicle.Rd flowCore/man/exponential-class.Rd flowCore/man/expressionFilter-class.Rd flowCore/man/fcReference-class.Rd flowCore/man/filter-and-methods.Rd flowCore/man/filter-class.Rd flowCore/man/filter-in-methods.Rd flowCore/man/filter-methods.Rd flowCore/man/filter-on-methods.Rd flowCore/man/filterDetails-methods.Rd flowCore/man/filterList-class.Rd flowCore/man/filterReference-class.Rd flowCore/man/filterResult-class.Rd flowCore/man/filterResultList-class.Rd flowCore/man/filterSet-class.Rd flowCore/man/filterSummary-class.Rd flowCore/man/filterSummaryList-class.Rd flowCore/man/filters-class.Rd flowCore/man/flowCore-package.Rd flowCore/man/flowFrame-class.Rd flowCore/man/flowSet-class.Rd flowCore/man/fsApply.Rd flowCore/man/gateActionItem-class.Rd flowCore/man/gateView-class.Rd flowCore/man/getChannelMarker.Rd flowCore/man/getIndexSort-methods.Rd flowCore/man/hyperlog-class.Rd flowCore/man/hyperlogtGml2-class.Rd flowCore/man/identifier-methods.Rd flowCore/man/inverseLogicleTransform.Rd flowCore/man/invsplitscale-class.Rd flowCore/man/keyword-methods.Rd flowCore/man/kmeansFilter.Rd flowCore/man/linearTransform.Rd flowCore/man/lintGml2-class.Rd flowCore/man/lnTransform.Rd flowCore/man/logTransform.Rd flowCore/man/logarithm-class.Rd flowCore/man/logicalFilterResult-class.Rd flowCore/man/logicleTransform.Rd flowCore/man/logicletGml2-class.Rd flowCore/man/logtGml2-class.Rd flowCore/man/manyFilterResult-class.Rd flowCore/man/markernames.Rd flowCore/man/multipleFilterResult-class.Rd flowCore/man/norm2Filter-class.Rd flowCore/man/normalization-class.Rd flowCore/man/normalizeActionItem-class.Rd flowCore/man/normalizeView-class.Rd flowCore/man/parameterFilter-class.Rd flowCore/man/parameterTransform-class.Rd flowCore/man/parameters-class.Rd flowCore/man/parameters-methods.Rd flowCore/man/polygonGate.Rd flowCore/man/polytopeGate.Rd flowCore/man/quadGate.Rd flowCore/man/quadratic-class.Rd flowCore/man/quadraticTransform.Rd flowCore/man/randomFilterResult-class.Rd flowCore/man/ratio-class.Rd flowCore/man/ratiotGml2-class.Rd flowCore/man/read.FCS.Rd flowCore/man/read.FCSheader.Rd flowCore/man/read.flowSet.Rd flowCore/man/rectangleGate.Rd flowCore/man/sampleFilter-class.Rd flowCore/man/scaleTransform.Rd flowCore/man/setOperationFilter-class.Rd flowCore/man/singleParameterTransform-class.Rd flowCore/man/sinht-class.Rd flowCore/man/spillover-flowSet.Rd flowCore/man/split-methods.Rd flowCore/man/splitScaleTransform.Rd flowCore/man/splitscale-class.Rd flowCore/man/squareroot-class.Rd flowCore/man/subsetting-class.Rd flowCore/man/subsettingActionItem-class.Rd flowCore/man/subsettingView-class.Rd flowCore/man/summarizeFilter-methods.Rd flowCore/man/timeFilter-class.Rd flowCore/man/transform-class.Rd flowCore/man/transformActionItem-class.Rd flowCore/man/transformFilter-class.Rd flowCore/man/transformList-class.Rd flowCore/man/transformMap-class.Rd flowCore/man/transformReference-class.Rd flowCore/man/transformView-class.Rd flowCore/man/transformation-class.Rd flowCore/man/truncateTransform.Rd flowCore/man/unitytransform-class.Rd flowCore/man/validFilters.Rd flowCore/man/view-class.Rd flowCore/man/workFlow-class.Rd flowCore/man/write.FCS.Rd flowCore/man/write.flowSet.Rd
flowCore/paper
flowCore/paper/Figure1-flowCoreFrameWork.jpg
flowCore/paper/Figure1.ppt
flowCore/paper/Figure2-flowWheel-version4.jpg
flowCore/paper/bmc_article.bib
flowCore/paper/bmc_article.bst
flowCore/paper/bmc_article.cls
flowCore/paper/bmc_article.tex
flowCore/paper/figure.R
flowCore/paper/flowCoreRef.bib
flowCore/paper/flowQ.jpg
flowCore/paper/manuscript.tex
flowCore/paper/outline.tex
flowCore/paper/response2reviewers.rtf
flowCore/paper/xyplot.pdf
flowCore/src
flowCore/src/FastLogicle.cpp
flowCore/src/Hyperlog.cpp
flowCore/src/Logicle.cpp
flowCore/src/Makevars
flowCore/src/RcppExports.cpp
flowCore/src/biexponential.cpp
flowCore/src/boost_regex
flowCore/src/boost_regex/README
flowCore/src/boost_regex/c_regex_traits.cpp
flowCore/src/boost_regex/c_regex_traits.o
flowCore/src/boost_regex/cpp_regex_traits.cpp
flowCore/src/boost_regex/cpp_regex_traits.o
flowCore/src/boost_regex/cregex.cpp
flowCore/src/boost_regex/cregex.o
flowCore/src/boost_regex/fileiter.cpp
flowCore/src/boost_regex/fileiter.o
flowCore/src/boost_regex/icu.cpp
flowCore/src/boost_regex/icu.o
flowCore/src/boost_regex/instances.cpp
flowCore/src/boost_regex/instances.o
flowCore/src/boost_regex/internals.hpp
flowCore/src/boost_regex/posix_api.cpp
flowCore/src/boost_regex/posix_api.o
flowCore/src/boost_regex/regex.cpp
flowCore/src/boost_regex/regex.o
flowCore/src/boost_regex/regex_debug.cpp
flowCore/src/boost_regex/regex_debug.o
flowCore/src/boost_regex/regex_raw_buffer.cpp
flowCore/src/boost_regex/regex_raw_buffer.o
flowCore/src/boost_regex/regex_traits_defaults.cpp
flowCore/src/boost_regex/regex_traits_defaults.o
flowCore/src/boost_regex/static_mutex.cpp
flowCore/src/boost_regex/static_mutex.o
flowCore/src/boost_regex/usinstances.cpp
flowCore/src/boost_regex/usinstances.o
flowCore/src/boost_regex/w32_regex_traits.cpp
flowCore/src/boost_regex/w32_regex_traits.o
flowCore/src/boost_regex/wc_regex_traits.cpp
flowCore/src/boost_regex/wc_regex_traits.o
flowCore/src/boost_regex/wide_posix_api.cpp
flowCore/src/boost_regex/wide_posix_api.o
flowCore/src/boost_regex/winstances.cpp
flowCore/src/boost_regex/winstances.o
flowCore/src/convertRawBytes.cpp
flowCore/src/convertRawBytes.h
flowCore/src/fcsTextParse.cpp
flowCore/src/flowCore_types.h
flowCore/src/hyperlog.h
flowCore/src/hyperlogTransform.cpp
flowCore/src/inPolygon.cpp
flowCore/src/inPolytope.cpp
flowCore/src/logicle.h
flowCore/src/logicleTransform.cpp
flowCore/src/pairVectorRcppWrap.cpp
flowCore/src/pairVectorRcppWrap.h
flowCore/src/sortBytes.cpp
flowCore/src/uint2double.cpp
flowCore/src/zeroin.cpp
flowCore/src/zeroin.h
flowCore/tests
flowCore/tests/testthat
flowCore/tests/testthat.R
flowCore/tests/testthat/IO-testSuite.R
flowCore/tests/testthat/expectResults.rds
flowCore/tests/testthat/helper-expectResults.R
flowCore/tests/testthat/test-classes.R
flowCore/tests/testthat/test-convertRawBytes.R
flowCore/tests/testthat/test-fcsTextParse.R
flowCore/tests/testthat/test-filter.R
flowCore/tests/testthat/test-flowSet-IO.R
flowCore/tests/testthat/test-gating.R
flowCore/tests/testthat/test-markernames.R
flowCore/tests/testthat/test-paramMatch.R
flowCore/tests/testthat/test-sortBytes.R
flowCore/tests/testthat/test-transform.R
flowCore/unitTests
flowCore/unitTests/InOutEventsTests
flowCore/unitTests/InOutEventsTests/ExpectedResult_Files
flowCore/unitTests/InOutEventsTests/FCS_Files
flowCore/unitTests/InOutEventsTests/Gating-ML_Files
flowCore/unitTests/InOutEventsTests/RUnitScript_Files
flowCore/unitTests/InvalidGateTests
flowCore/unitTests/InvalidGateTests/FCS_Files
flowCore/unitTests/InvalidGateTests/Gating-ML_Files
flowCore/unitTests/InvalidGateTests/RUnitScript_Files
flowCore/unitTests/ValidGateTests
flowCore/unitTests/ValidGateTests/Gating-ML_Files
flowCore/vignettes
flowCore/vignettes/HowTo-flowCore.Rnw
flowCore/vignettes/cytoref.bib
flowCore/vignettes/fcs3.html

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