Representing Flow Cytometry Data with ncdfFlowSet | Creating a ncdfFlowSet | Working with metadata | Manipulating a ncdfFlowSet | Compensation,Transformation and Gating | Subsetting
Package: ncdfFlow 2.59.1
Mike Jiang
ncdfFlow: ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.
Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.
Authors:
ncdfFlow_2.59.1.tar.gz
ncdfFlow_2.59.1.zip(r-4.7)ncdfFlow_2.59.1.zip(r-4.6)ncdfFlow_2.59.1.zip(r-4.5)
ncdfFlow_2.59.1.tgz(r-4.6-x86_64)ncdfFlow_2.59.1.tgz(r-4.6-arm64)ncdfFlow_2.59.1.tgz(r-4.5-x86_64)ncdfFlow_2.59.1.tgz(r-4.5-arm64)
ncdfFlow_2.59.1.tar.gz(r-4.7-arm64)ncdfFlow_2.59.1.tar.gz(r-4.7-x86_64)ncdfFlow_2.59.1.tar.gz(r-4.6-arm64)ncdfFlow_2.59.1.tar.gz(r-4.6-x86_64)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ncdfFlow/json (API)
| # Install 'ncdfFlow' in R: |
| install.packages('ncdfFlow', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Uses libs:
On BioConductor:ncdfFlow-2.59.1(bioc 3.24)ncdfFlow-2.58.0(bioc 3.23)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyflowcytometrycurlopensslcpp
Last updated from:7e2647d555. Checks:1 ERROR, 11 WARNING, 1 OK, 1 FAIL. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 304 | ||
| linux-devel-arm64 | WARNING | 322 | ||
| linux-devel-x86_64 | WARNING | 395 | ||
| source / vignettes | OK | 611 | ||
| linux-release-arm64 | WARNING | 305 | ||
| linux-release-x86_64 | WARNING | 384 | ||
| macos-release-arm64 | WARNING | 116 | ||
| macos-release-x86_64 | WARNING | 313 | ||
| macos-oldrel-arm64 | WARNING | 200 | ||
| macos-oldrel-x86_64 | WARNING | 246 | ||
| windows-devel | WARNING | 274 | ||
| windows-release | WARNING | 479 | ||
| windows-oldrel | WARNING | 235 | ||
| wasm-release | FAIL | 866 |
Exports:as.flowSetclone.ncdfFlowSetcolnamescolnames<-compensatefiltergetFileNamegetIndicesinitIndiceskeywordkeyword<-lapplyload_ncfsmarkernamesmarkernames<-ncdfFlowListncdfFlowSetncfsApplypDatapData<-phenoDataphenoData<-rbind2read.ncdfFlowSetsampleNames<-save_ncfssplitSubsettransformunlinkupdateIndices
Dependencies:BHBiobaseBiocGenericsbiocmakecpp11cytolibdir.expiryfilelockflowCoregenericsmatrixStatsRcppRhdf5libRProtoBufLibS4Vectors
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| subsetting by sampleNames,channels(not for events) methods | [,ncdfFlowList,ANY-method [,ncdfFlowSet,ANY-method |
| extract a 'flowFrame' object from 'ncdfFlowSet' | [[,ncdfFlowList,character,missing-method [[,ncdfFlowList,character-method [[,ncdfFlowList,logical-method [[,ncdfFlowList,numeric-method [[,ncdfFlowSet,ANY-method |
| convert from a 'ncdfFlowSet' to a 'flowSet' | as.flowSet |
| Clone a ncdfFlowSet | clone.ncdfFlowSet |
| Accessors compatible with those for 'flowSet' | colnames,ncdfFlowList-method colnames<- colnames<-,ncdfFlowList-method colnames<-,ncdfFlowSet,ANY-method colnames<-,ncdfFlowSet-method compensate,flowSet,data.frame-method compensate,ncdfFlowSet,ANY-method compensate,ncdfFlowSet,list-method filter,ncdfFlowList,filter-method filter,ncdfFlowList,filterList-method filter,ncdfFlowList,list-method keyword,ncdfFlowSet,list-method keyword<-,ncdfFlowSet,list-method length,ncdfFlowList-method markernames,ncdfFlowList-method markernames<-,ncdfFlowList-method pData,ncdfFlowList-method pData<-,ncdfFlowList,data.frame-method phenoData,ncdfFlowList-method phenoData<-,ncdfFlowList,AnnotatedDataFrame-method sampleNames,ncdfFlowList-method sampleNames<- sampleNames<-,ncdfFlowSet,ANY-method transform,ncdfFlowSet-method |
| get the cdf file name associated with ncdfFlowSet object | getFileName |
| 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet | getIndices getIndices,ncdfFlowSet,character-method initIndices initIndices,ncdfFlowSet-method updateIndices updateIndices,ncdfFlowSet,character,logical-method |
| lapply method for ncdfFlowList | lapply,ncdfFlowList-method |
| ncdfFlow: A package that provides CDF storage based flow cytometry data analysis. | ncdfFlow |
| a class that stores multiple ncdfFlowSet objects | ncdfFlowList ncdfFlowList-class show,ncdfFlowList-method |
| a class for storing flow cytometry raw data in HDF5 format | ncdfFlowSet-class show show,ncdfFlowSet-method |
| create ncdfFlowSet from flowSet | ncdfFlowSet ncdfFlowSet,flowSet-method |
| apply method for ncdfFlowSet (for internal use) | ncfsApply ncfsApply,ncdfFlowSet-method |
| combine multiple ncdfFlowSet objects into one | rbind2,ncdfFlowList,ANY-method |
| create ncdfFlowSet from FCS files | read.ncdfFlowSet read.ncdfFlowset |
| write the flow data from a 'flowFrame' to 'ncdfFlowSet' flowFrame can have less channels than ncdfFlowSet,which is used for partial updating(useful for 'normalization') | replacement method for ncdfFlowSet [[<-,ncdfFlowSet,ANY,ANY,flowFrame-method [[<-,ncdfFlowSet,flowFrame-method |
| save/load a ncdfFlowSet object to/from disk. | load_ncfs save_ncfs |
| split a 'ncdfFlowSet' object. | split,ncdfFlowList,character-method split,ncdfFlowList,factor-method split,ncdfFlowSet,character-method split,ncdfFlowSet,factor-method split,ncdfFlowSet,filter-method split,ncdfFlowSet,filterResultList-method split,ncdfFlowSet,list-method |
| subset a ncdfFlowSet by filter | Subset,ncdfFlowList,filter-method Subset,ncdfFlowList,filterResultList-method Subset,ncdfFlowSet,filter-method Subset,ncdfFlowSet,filterResultList-method Subset,ncdfFlowSet,list-method |
| subset the ncdfFlowSet/ncdfFlowList based on 'pData' | subset.ncdfFlowList subset.ncdfFlowSet |
| delete the cdf file associated with the ncdfFlowSet object ncdfFlowSet object is unrecoverable after cdf is deleted. So this method is usually called when ncdfFlowSet object is no longer in need. | unlink,ncdfFlowSet-method |
