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

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

This package extends the flowCore infrastructure by storing the large volume of event-level data on disk as HDF format and only keeps the file handler and meta data in memory. Thus the memory consumption is significantly reduced.

INSTALLATION

library(knitr)
opts_chunk$set(message = FALSE, warning = FALSE, fig.height= 3, fig.width= 5)

# First, install it from bionconductor so that it will pull all the dependent packages automatically
library(BiocInstalller)
bicLite(ncdfFlow) 

# or install the latest version from github using devtools package 
install.packages("devtools") 
library(devtools) #load it
install_github("RGLab/ncdfFlow", ref="trunk")

Unix/Linux/Mac users

To build the ncdfFlow package from source, make sure that HDF5 Library is present on your system:

If HDF5 is installed to some non-standard location, you may pass the environment variable --with-hdf5 to point to the correct location of HDF5, for example,

#install from github
install_github('RGLab/ncdfFlow', ref='trunk', args='--configure-args="--with-hdf5=<path-to-hdf>"')

#or install from locally downloaded tar ball
R CMD INSTALL ncdfFlow_x.y.z.tar.gz --configure-args="--with-hdf5='<path-to-hdf>'"

under '/path/to', you should find "include" and "lib" sub-folders that contain HDF5 headers and shared libraries.

Also, make sure add the path of libhdf5.so (should be lib subfolder of <path-to-hdf>) to your environment variable LD_LIBRARY_PATH so that it can be found at runtime.

export LD_LIBRARY_PATH=<path-to-hdf>/lib:LD_LIBRARY_PATH

Create ncdfFlowSet object

library(ncdfFlow)

#read from FCS files
path <- system.file("extdata","compdata","data",package="flowCore")
files <- list.files(path,full.names=TRUE)[1:3]
fs <- read.ncdfFlowSet(files=files) #equivalent to flowCore::read.flowSet


#or convert the existing flowSet into ncdfFlowSet
data(GvHD)
fs <- GvHD[1:4]
fs <- ncdfFlowSet(fs)
fs

Use it as the same way as flowSet (except it is memory efficient and fast)

pData(fs)
sampleNames(fs)
keyword(fs,"FILENAME")
colnames(fs)
length(fs)
fs[[1]]
fs[2:3]

RGLab/ncdfFlow documentation built on Jan. 14, 2025, 6:19 a.m.