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",
      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

[Package ncdfFlow version 2.30.1 Index]