extract a flowFrame object from ncdfFlowSet

Description

Simliar to [[, and there are cerntain ways to reduce the disk IO and optimize the speed.

Usage

## S4 method for signature 'ncdfFlowSet,ANY'
x[[i, j, use.exprs = TRUE, ...]]

## S4 method for signature 'ncdfFlowList,numeric'
x[[i, j, ...]]

## S4 method for signature 'ncdfFlowList,logical'
x[[i, j, ...]]

## S4 method for signature 'ncdfFlowList,character'
x[[i, j, ...]]

Arguments

Examples

data(GvHD)
nc <- ncdfFlowSet(GvHD[1:2])
samples <- sampleNames(nc)
sn <- samples[1]
#return the entire flowFrame
fr <- nc[[sn]]

#access the flowFrame meta data without loading the raw event data from disk
nc[[sn, use.exprs = FALSE]]

#only read a subset of channels (more efficient than reading entire data set)
nc[[sn, 1:2]]

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/extractFlowFrame.Rd_%03d_medium.png", width=480, height=480)
> ### Name: [[,ncdfFlowSet,ANY-method
> ### Title: extract a 'flowFrame' object from 'ncdfFlowSet'
> ### Aliases: [[,ncdfFlowList,character,missing-method
> ###   [[,ncdfFlowList,character-method [[,ncdfFlowList,logical-method
> ###   [[,ncdfFlowList,numeric-method [[,ncdfFlowSet,ANY-method
> 
> ### ** Examples
> 
> data(GvHD)
> nc <- ncdfFlowSet(GvHD[1:2])
write s5a01 to empty cdf slot...
write s5a02 to empty cdf slot...
> samples <- sampleNames(nc)
> sn <- samples[1]
> #return the entire flowFrame
> fr <- nc[[sn]]
> 
> #access the flowFrame meta data without loading the raw event data from disk
> nc[[sn, use.exprs = FALSE]]
flowFrame object 's5a01'
with 0 cells and 0 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         CD15 FITC  1024        1    10000
$P4 FL2-H           CD45 PE  1024        1    10000
$P5 FL3-H        CD14 PerCP  1024        1    10000
$P6 FL2-A              <NA>  1024        0     1023
$P7 FL4-H          CD33 APC  1024        1    10000
$P8  Time Time (51.20 sec.)  1024        0     1023
153 keywords are stored in the 'description' slot
> 
> #only read a subset of channels (more efficient than reading entire data set)
> nc[[sn, 1:2]]
flowFrame object 's5a01'
with 3420 cells and 2 observables:
     name       desc range minRange maxRange
$P1 FSC-H FSC-Height  1024        0     1023
$P2 SSC-H SSC-Height  1024        0     1023
153 keywords are stored in the 'description' slot
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>