getIndices extracts the event indices of one or multiple samples from ncdfFlowSet

Description

These functions are mainly for internal usage and normally not to be used by users.

initIndices initializes the event indices for the entire ncdfFlowSet with NA

updateIndices updates the event indices of the target sample in ncdfFlowSet

Usage

## S4 method for signature 'ncdfFlowSet,character'
getIndices(obj, y)

## S4 method for signature 'ncdfFlowSet'
initIndices(obj)

## S4 method for signature 'ncdfFlowSet,character,logical'
updateIndices(obj, y, z)

Arguments

Value

a logical vector.

Examples

data(GvHD)
nc <- ncdfFlowSet(GvHD[1:2])
sn <- sampleNames(nc)[1]
nrow(nc[[sn]])
getIndices(nc, sn) #initial index is NA
#subset with filter
morphGate <- norm2Filter("FSC-H", "SSC-H", filterId = "MorphologyGate",scale = 2)
nc1 <- Subset(nc, morphGate)
ind <- getIndices(nc1, sn)
all.equal(sum(ind), nrow(nc1[[sn]]))
initIndices(nc1)
getIndices(nc1, sn) #reset indices

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/Indices.Rd_%03d_medium.png", width=480, height=480)
> ### Name: getIndices,ncdfFlowSet,character-method
> ### Title: 'getIndices' extracts the event indices of one or multiple
> ###   samples from ncdfFlowSet
> ### Aliases: getIndices getIndices,ncdfFlowSet,character-method initIndices
> ###   initIndices,ncdfFlowSet-method updateIndices
> ###   updateIndices,ncdfFlowSet,character,logical-method
> 
> ### ** Examples
> 
> data(GvHD)
> nc <- ncdfFlowSet(GvHD[1:2])
write s5a01 to empty cdf slot...
write s5a02 to empty cdf slot...
> sn <- sampleNames(nc)[1]
> nrow(nc[[sn]])
[1] 3420
> getIndices(nc, sn) #initial index is NA
[1] NA
> #subset with filter
> morphGate <- norm2Filter("FSC-H", "SSC-H", filterId = "MorphologyGate",scale = 2)
> nc1 <- Subset(nc, morphGate)
> ind <- getIndices(nc1, sn)
> all.equal(sum(ind), nrow(nc1[[sn]]))
[1] TRUE
> initIndices(nc1)
> getIndices(nc1, sn) #reset indices
[1] NA
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>