Package: flowStats 4.25.0

Greg Finak

flowStats: Statistical methods for the analysis of flow cytometry data

Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.

Authors:Florian Hahne, Nishant Gopalakrishnan, Alireza Hadj Khodabakhshi, Chao-Jen Wong, Kyongryun Lee

flowStats_4.25.0.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
flowStats/json (API)

# Install 'flowStats' in R:

install.packages('flowStats', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/rglab/flowstats/issues

Datasets:

BackGating - Sample backgating results
ITN - Sample flow cytometry data

On BioConductor:flowStats-4.25.0(bioc 3.24)flowStats-4.24.0(bioc 3.23)

immunooncology flowcytometry cellbasedassays

9.19 score 15 stars 2 packages 336 scripts 2.3k downloads 19 mentions 31 exports 92 dependencies

Last updated from:78c4b7cdd2. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	187
linux-devel	WARNING	331
source / vignettes	OK	482
linux-release	WARNING	284
macos-release	WARNING	230
macos-oldrel	WARNING	204
windows-devel	WARNING	224
windows-release	WARNING	228
windows-oldrel	WARNING	216
wasm-release	OK	139

Exports:%in%binByRef calcPBChiSquare calcPearsonChi curv1Filter curv2Filter curvPeaks flowClust2Prior gate_singlet gaussNorm gpaSet iProcrustes lymphGate mkPrior norm2Filter normalize normQA oneDGate overton_like plotBins plotPrior proBin quadrantGate rangeFilter rangeGate SimulateMixture singletGate spillover spillover_match spillover_ng warpSet

Dependencies:abind ash BH Biobase BiocGenerics biocmake bitops cli clue cluster colorspace corpcor cpp11 cytolib data.table DelayedArray deldir DEoptimR deSolve dir.expiry dplyr farver fda fds filelock flowCore flowViz flowWorkspace FNN generics ggplot2 glue graph gtable hdrcde hexbin IDPmisc interp IRanges isoband jpeg kernlab KernSmooth ks labeling lattice latticeExtra lifecycle locfit magrittr MASS Matrix MatrixGenerics matrixStats mclust mgcv mnormt multicool mvtnorm ncdfFlow nlme pcaPP pillar pkgconfig png pracma R6 rainbow RBGL RColorBrewer Rcpp RcppEigen RCurl Rgraphviz Rhdf5lib rlang robustbase RProtoBufLib rrcov S4Arrays S4Vectors S7 scales SparseArray tibble tidyselect utf8 vctrs viridisLite withr XML XVector

flowStats Overview

Introduction | Probability Binning

Rendered fromGettingStartedWithFlowStats.Rnwusingutils::Sweave

Last update: 2019-11-26
Started: 2013-12-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Statistical methods for flow cytometry data analysis	flowStats-package flowStats
These methods are copied from flowViz to eliminate its dependency on curv1Filter and curv2Filter	addName,curv1Filter,character-method addName,curv1Filter,logical-method addName,curv2Filter,character-method addName,curv2Filter,logical-method
Automated gating of single populations in 2D	autoGate
Sample backgating results	BackGating
Bin a test data set using bins previously created by probability binning a control dataset	binByRef
Probability binning metirc for comparing the probability binned datasets	calcPBChiSquare
Pearsons chi-square statistic for comparing the probability binned datasets	calcPearsonChi
Class "curv1Filter"	%in%,flowFrame,curv1Filter-method curv1Filter curv1Filter-class show,curv1Filter-method summarizeFilter,multipleFilterResult,curv1Filter-method
Class "curv2Filter"	%in%,flowFrame,curv2Filter-method curv2Filter curv2Filter-class show,curv2Filter-method summarizeFilter,multipleFilterResult,curv2Filter-method
Parse curv1Filter output	curvPeaks
Find most likely separation between positive and negative populations in 1D	density1d
convert ellipse from cov/mu to points used to plot priors	ellipse
The version of fdPar from fda 2.4.0 because the new API changes the output. (specifically res$fd$coefs) and thus breaks the landmarkreg call.	fdPar
Generate a prior specification based on a flowClust model This function generates a prior specification based on a flowClust fit object It can be passed to a second round of flowClust() with usePrior="yes" The prior could be estimated from a single sample, for example, and then used to speed up the convergence for other samples.	flowClust2Prior
Creates a singlet polygon gate using the prediction bands from a robust linear model	gate_singlet singletGate
Per-channel normalization based on landmark registration	gaussNorm
Multi-dimensional normalization of flow cytometry data	gpaSet
(Internal use only) Identify features of flow cytometry data using backgating	idFeatures idFeaturesByBackgating
Procrustes analysis. Using singular value decomposition (SVD) to determine a linear transformation to align the points in X to the points in a reference matrix Y.	iProcrustes
Sample flow cytometry data	ITN
Compute and cluster high density regions in 1D	landmarkMatrix
Automated gating of elliptical cell populations in 2D.	%in%,flowFrame,lymphFilter-method lymphFilter lymphFilter-class lymphGate
Generate a flowClust prior specification	mkPrior mkPrior,list,flowSet,ANY,missing-method mkPrior,list,flowSet,missing,missing-method mkPrior,missing,flowFrame,missing,missing-method mkPrior,missing,flowSet,ANY,missing-method mkPrior,polygonGate,flowFrame,missing,missing-method mkPrior,polygonGate,flowFrame,numeric,matrix-method mkPrior,rectangleGate,flowFrame,missing,missing-method mkPrior,rectangleGate,flowFrame,numeric,matrix-method
Class "norm2Filter"	%in%,flowFrame,norm2Filter-method norm2Filter norm2Filter-class show,norm2Filter-method
normalize a GatingSet imported with flowWorkspace, using sequential normalization on the manual gates in the GatingHierarchy.	normalize normalize,GatingSet,missing-method normalize,GatingSetInternal,missing-method normalize-methods
Normalization quality assessment	normQA
Overton-like subtraction of densities.	overton_like
Plots the probability bins overlaid with flowFrame data	plotBins
Plots a flowClust prior over some data.	plotPrior
Probability binning - a metric for evaluating multivariate differences	proBin
Automated quad gating	quadrantGate
Find most likely separation between positive and negative populations in 1D	%in%,flowFrame,rangeFilter-method oneDGate rangeFilter rangeFilter-class rangeGate
Random Generation from a t Mixture Model with Box-Cox Transformation	SimulateMixture
Construct a 'flowSet' for use with 'spillover' by matching channel names to compensation control filenames	spillover_match spillover_match,flowSet-method spillover_match,missing-method spillover_match-flowSet
Compute a spillover matrix from a 'flowSet', simplified API	spillover_ng spillover_ng,flowSet-method spillover_ng,missing-method spillover_ng-flowSet
Compute a spillover matrix from a flowSet	spillover spillover,flowSet-method spillover-flowSet
Normalization based on landmark registration	warpSet warpSet.cytoset warpSetGS warpSetNCDF warpSetNCDFLowMem