Clone a ncdfFlowSet

Description

Create a new ncdfFlowSet object from an existing one

Usage

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

Arguments

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,by default the actual raw data is not added
nc2<-clone.ncdfFlowSet(nc1,"clone.nc")
nc2[[1]]

#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)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(ncdfFlow)
Loading required package: flowCore
Loading required package: flowViz
Loading required package: lattice
Loading required package: RcppArmadillo
Loading required package: BH
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/ncdfFlow/clone.ncdfFlowSet.Rd_%03d_medium.png", width=480, height=480)
> ### Name: clone.ncdfFlowSet
> ### Title: Clone a ncdfFlowSet
> ### Aliases: clone.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)
All FCS files have the same following channels:
FSC-H
SSC-H
FL1-H
FL2-H
FL3-H
FL1-A
FL4-H
write 060909.001 to empty cdf slot...
write 060909.002 to empty cdf slot...
write 060909.003 to empty cdf slot...
done!
> 
> ##clone the ncdfFlowSet object,by default the actual raw data is not added
> nc2<-clone.ncdfFlowSet(nc1,"clone.nc")
> nc2[[1]]
flowFrame object '060909.001'
with 0 cells and 7 observables:
     name       desc range minRange maxRange
$P1 FSC-H FSC-Height  1024        0     1023
$P2 SSC-H SSC-Height  1024        0     1023
$P3 FL1-H       <NA>  1024        1    10000
$P4 FL2-H       <NA>  1024        1    10000
$P5 FL3-H       <NA>  1024        1    10000
$P6 FL1-A       <NA>  1024        0     1023
$P7 FL4-H       <NA>  1024        1    10000
139 keywords are stored in the 'description' slot
> 
> #add the actual raw data
> fs1  <- read.flowSet(files=files)
> nc2[[sampleNames(fs1)[1]]] <- fs1[[1]]
write 060909.001 to empty cdf slot...
> nc2[[1]]
flowFrame object '060909.001'
with 10000 cells and 7 observables:
     name       desc range minRange maxRange
$P1 FSC-H FSC-Height  1024        0     1023
$P2 SSC-H SSC-Height  1024        0     1023
$P3 FL1-H       <NA>  1024        1    10000
$P4 FL2-H       <NA>  1024        1    10000
$P5 FL3-H       <NA>  1024        1    10000
$P6 FL1-A       <NA>  1024        0     1023
$P7 FL4-H       <NA>  1024        1    10000
141 keywords are stored in the 'description' slot
> 
> #delete the cdf file associated with ncdfFlowSet before removing it from memory
> unlink(nc2)
> rm(nc2)
> 
> unlink(nc1)
> rm(nc1)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>