clone.ncdfFlowSet: Clone a ncdfFlowSet

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

Description

Create a new ncdfFlowSet object from an existing one

Usage

clone.ncdfFlowSet(
  ncfs,
  ncdfFile = NULL,
  isEmpty = FALSE,
  isNew = TRUE,
  dim = 2,
  compress = 0
)

Arguments

ncfs	A ncdfFlowSet.
ncdfFile	A character scalar giving the output file name. By default, It is NULL and the function will generate a random file name, potentially adding the .cdf suffix unless a file extension is already present. It is only valid when isNewNcFile=TRUE
isEmpty	A logical scalar indicating whether the raw data should also be copied.if FALSE, an empty cdf file is created with the same dimensions (sample*events*channels) as the orignial one.
isNew	A logical scalar indicating whether the new cdf file should be created. If FALSE, the original cdf file is associated with the new ncdfFlowSet object.
dim	integer see details in read.ncdfFlowset.
compress	integer see details in read.ncdfFlowset.

Value

A ncdfFlowSet object

See Also

read.ncdfFlowSet

Examples

path<-system.file("extdata","compdata","data",package="flowCore")
files<-list.files(path,full.names=TRUE)[1:3]

#create ncdfFlowSet from fcs
nc1  <- read.ncdfFlowSet(files=files,ncdfFile="ncfsTest.nc",flowSetId="fs1",isWriteSlice= TRUE)

##clone the ncdfFlowSet object
nc2<-clone.ncdfFlowSet(nc1,"clone.nc")
nc2[[1]]

#optionally create the empty hdf file without writting the acutal flow data into it
nc2 <- clone.ncdfFlowSet(nc1,"clone.nc", isEmpty = TRUE)

#add the actual raw data
fs1  <- read.flowSet(files=files)
nc2[[sampleNames(fs1)[1]]] <- fs1[[1]]
nc2[[1]]

#delete the cdf file associated with ncdfFlowSet before removing it from memory
unlink(nc2)
rm(nc2)

unlink(nc1)
rm(nc1)

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