Package: flowMerge 2.61.0

Greg Finak

flowMerge: Cluster Merging for Flow Cytometry Data

Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.

Authors:Greg Finak <[email protected]>, Raphael Gottardo <[email protected]>

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
flowMerge/json (API)

# Install 'flowMerge' in R:

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

Datasets:

flowClust.res - A flowClust model fitted to the rituximab data for 1:10 clusters.

On BioConductor:flowMerge-2.61.0(bioc 3.24)flowMerge-2.60.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncology clustering flowcytometry

4.56 score 1 packages 6 scripts 470 downloads 6 mentions 16 exports 41 dependencies

Last updated from:44577eca6f. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	178
linux-devel-x86_64	WARNING	281
source / vignettes	OK	248
linux-release-x86_64	WARNING	292
macos-release-arm64	WARNING	110
macos-oldrel-arm64	WARNING	135
windows-devel	WARNING	165
windows-release	WARNING	159
windows-oldrel	WARNING	163
wasm-release	OK	133

Exports:BIC checkForRemoteErrors ENT fitPiecewiseLinreg flowObj getData ICL map merge NENT pFlowMerge plot ptree show split summary

Dependencies:BH Biobase BiocGenerics biocmake codetools cpp11 cytolib DEoptimR dir.expiry feature filelock flowClust flowCore FNN foreach generics graph iterators kernlab KernSmooth ks lattice Matrix matrixStats mclust mgcv misc3d multicool mvtnorm nlme pcaPP plot3D pracma Rcpp Rgraphviz Rhdf5lib robustbase RProtoBufLib rrcov S4Vectors snow

Merging Mixture Components for Cell Population Identification in Flow Cytometry Data The flowMerge package

Rendered fromflowmerge.Rmdusingknitr::rmarkdown

Last update: 2019-04-04
Started: 2019-04-04

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Merging of mixture components for automated gating of flow cytometry data.	flowMerge-package flowMerge
Check output of snow clusters for errors	checkForRemoteErrors
Fit Piecewise Linear Regression for a list of flowMerge Objects	fitPiecewiseLinreg
Methods for fitPiecewiseLinreg in flowMerge package	fitPiecewiseLinreg,list-method fitPiecewiseLinreg-methods
Update the flagOutliers slot in a flowMerge object	flagOutliers
Methods to update the flagOutliers slot in a flowMerge object.	flagOutliers,flowMerge-method flagOutliers-methods
A flowClust model fitted to the rituximab data for 1:10 clusters.	flowClust.res RituximabFlowClustFit
Class "flowMerge"	flowMerge-class getData,flowMerge-method plot,flowMerge,missing-method
Create a flowObj object from a flowClust and flowFrame object	flowObj
Class "flowObj"	flowObj-class getData,flowObj-method merge,flowObj,missing-method plot,flowObj,missing-method
Initialize a SNOW cluster for use with flowMerge	initPFlowMerge
Map matrix of probabilities to class assignments.	map
Merge clusters in flow cytometry data	merge merge,flowObj merge,flowObj,metric
Merge mixture components	merge,flowObj-methods merge-methods
Cluster merging not meant to be called by the user	mergeClusters
Cluster merging not meant to be called by the user	mergeClusters2
Extract the Normalized Entropy	NENT
Parallelized FlowClust	pFlowClust
Parellel call to flowMerge	pFlowMerge
Methods for plotting flowMerge and flowObj classes	plot,flowMerge plot,flowObj plot-methods
Generate a Function to Plot The Merging Tree	ptree
Describe a flowObj or flowMerge object	show,flowMerge-method show,flowObj-method
Split data in a flowMerge object by cluster	split,flowMerge,missing-method split-methods
Summary methods for flowMerge	summary,flowMerge-method summary,flowObj-method
Update uncertainties	updateU