ncdfFlow (version 2.18.0)

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

Description

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

Usage

"[["(x, i, j = "missing", only.exprs = FALSE, compress = 0, ...) <- value

Arguments

x

a ncdfFlowSet

i

a numeric or character used as sample index of ncdfFlowSet

j

not used

only.exprs

a logical Default is FALSE. which will update the parameters and decriptions slot as well as the raw data. Sometime it is more efficient ti set it to TRUE skip the overhead of colnames matching and updating when user is only concerned about raw data instead of the entire flowFrame.

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
nc[[sn, only.exprs = TRUE]] <- fr_trans