replacement-method-for-ncdfFlowSet: write the flow data from a 'flowFrame' to 'ncdfFlowSet'...

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

Description

write the flow data from a flowFrame to ncdfFlowSet

flowFrame can have less channels than ncdfFlowSet,which is used for partial updating(useful for normalization)

Usage

## S4 replacement method for signature 'ncdfFlowSet,ANY,ANY,flowFrame'
x[[i, j = "missing", compress = 0, ...]] <- value

Arguments

x	a ncdfFlowSet
i	a numeric or character used as sample index of ncdfFlowSet
j	not used
compress	integer It is only relevant to writing slice to '2d' format because the compression is set during the creation of hdf5 file for '3d' format. see details in read.ncdfFlowset.
...	not used
value	flowFrame

Examples

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

#transform the data
lgcl <- logicleTransform( w = 0.5, t= 10000, m =4.5)
fr_trans <- transform(fr, `FL1-H` = lgcl(`FL1-H`), `FL2-H` = lgcl(`FL2-H`))

#update the data
nc[[sn]] <- fr_trans
apply(exprs(nc[[sn]]), 2, range)

#subset on channels
nc1 <- nc[,2:3]
#only write the channels of interest (reduce disk IO)
nc1[[sn]] <- fr_trans[,2:3]

#chanel colnames
colnames(fr_trans)[3:4] <- c("<FL1-H>", "<FL2-H>")

#write data without matching up the colnames will fail 
#nc[[sn]] <- fr_trans

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