Indices: 'getIndices' extracts the event indices of one or multiple...

Description Usage Arguments Value Examples

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

1
2
3
4
5
6
7
8
## 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

obj

ncdfFlowSet object

y

character sample name

z

logical vector to be assigned.

Value

a logical vector.

Examples

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
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

Bioconductor-mirror/ncdfFlow documentation built on July 12, 2017, 9:05 a.m.