flowCore: flowCore: Basic structures for flow cytometry data

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

Author
B. Ellis, P. Haaland, F. Hahne, N. Le Meur, N. Gopalakrishnan, J. Spidlen, M. Jiang
Date of publication
None
Maintainer
M.Jiang <wjiang2@fhcrc.org>
License
Artistic-2.0
Version
1.40.3

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