replacement method for ncdfFlowSet {ncdfFlow} | R Documentation

## 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`)

### 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

[Package ncdfFlow version 2.38.0 Index]