# ncdfFlow: A package that provides HDF5 based storage for flow cytometry data.

## Documentation for package ‘ncdfFlow’ version 2.36.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

as.flowSet | convert from a 'ncdfFlowSet' to a 'flowSet'
clone.ncdfFlowSet | Clone a ncdfFlowSet
colnames-method | Accessors compatible with those for 'flowSet'
colnames<- | Accessors compatible with those for 'flowSet'
colnames<--method | Accessors compatible with those for 'flowSet'
compensate-method | Accessors compatible with those for 'flowSet'
filter-method | Accessors compatible with those for 'flowSet'
getFileName | get the cdf file name associated with ncdfFlowSet object
getIndices | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
getIndices-method | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
initIndices | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
initIndices-method | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
keyword-method | Accessors compatible with those for 'flowSet'
keyword<--method | Accessors compatible with those for 'flowSet'
lapply-method | lapply method for ncdfFlowList
length-method | Accessors compatible with those for 'flowSet'
load_ncfs | save/load a ncdfFlowSet object to/from disk.
markernames-method | Accessors compatible with those for 'flowSet'
markernames<--method | Accessors compatible with those for 'flowSet'
ncdfFlow | ncdfFlow: A package that provides CDF storage based flow cytometry data analysis.
ncdfFlowList | a class that stores multiple ncdfFlowSet objects
ncdfFlowList-class | a class that stores multiple ncdfFlowSet objects
ncdfFlowSet | create ncdfFlowSet from flowSet
ncdfFlowSet-class | a class for storing flow cytometry raw data in HDF5 format
ncdfFlowSet-method | create ncdfFlowSet from flowSet
ncfsApply | apply method for ncdfFlowSet (for internal use)
ncfsApply-method | apply method for ncdfFlowSet (for internal use)
pData-method | Accessors compatible with those for 'flowSet'
pData<--method | Accessors compatible with those for 'flowSet'
phenoData-method | Accessors compatible with those for 'flowSet'
phenoData<--method | Accessors compatible with those for 'flowSet'
rbind2-method | combine multiple ncdfFlowSet objects into one
read.ncdfFlowSet | create ncdfFlowSet from FCS files
read.ncdfFlowset | create ncdfFlowSet from FCS files
replacement method for 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')
sampleNames-method | Accessors compatible with those for 'flowSet'
sampleNames<- | Accessors compatible with those for 'flowSet'
sampleNames<--method | Accessors compatible with those for 'flowSet'
save_ncfs | save/load a ncdfFlowSet object to/from disk.
show | a class for storing flow cytometry raw data in HDF5 format
show-method | a class that stores multiple ncdfFlowSet objects
show-method | a class for storing flow cytometry raw data in HDF5 format
split-method | split a 'ncdfFlowSet' object.
Subset-method | subset a ncdfFlowSet by filter
subset.ncdfFlowList | subset the ncdfFlowSet/ncdfFlowList based on 'pData'
subset.ncdfFlowSet | subset the ncdfFlowSet/ncdfFlowList based on 'pData'
transform-method | Accessors compatible with those for 'flowSet'
unlink-method | 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.
updateIndices | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
updateIndices-method | 'getIndices' extracts the event indices of one or multiple samples from ncdfFlowSet
[-method | subsetting by sampleNames,channels(not for events) methods
[[-method | extract a 'flowFrame' object from 'ncdfFlowSet'
[[<--method | 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')