ncdfFlowSet-class: a class for storing flow cytometry raw data in HDF5 format

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

Description

This class is a subclass of flowSet. It stores the raw data in cdf file instead of memory so that the analysis tools provided by flowCore based packages can be used in the study that produces hundreds or thousands FCS files.

Usage

## S4 method for signature 'ncdfFlowSet'
show(object)

Arguments

object

ncdfFlowSet show,ncdfFlowSet-method

Slots

file:

A character containing the ncdf file name.

maxEvents:

An integer containing the maximum number of events of all samples stored in this ncdfFlowSet object

flowSetId:

A character for the id of ncdfFlowSet object

indices:

Object of class "environment" containing events indices of each sample stored as "raw" vector. Each index value is either TURE or FALSE and the entire indices vector is used to subset the raw data. the indices vector of each sample is NA by default when the ncdfFlowSet first created.It is assigned with actual value when ncdfFlowSet object is subsetted by Subset or other subsetting methods.

origSampleVector:

A character vector containing the sample names, which indicates the original order of samples physically stored in cdf format

origColnames:

A character vector containing the flow channel names, which indicates the original order of columns physically stored in cdf format

frames:

Object of class "environment", which replicates the "frame" slot in flowSet, except that exprs matrix is empty and the actual data is stored in cdf file.

phenoData:

see phenoData

Extends

Class "flowSet", directly.

ncdfFlow documentation built on Nov. 8, 2020, 7:52 p.m.