FlowSOMSubset {FlowSOM} | R Documentation

## FlowSOM subset

### Description

Take a subset from a FlowSOM object

### Usage

    FlowSOMSubset(fsom, ids)

### Arguments

`fsom` | FlowSOM object, as generated by `BuildMST`
`ids` | Array containing the ids to keep

### Value

FlowSOM object containg updated data and medianvalues, but with the same grid

### See Also

`BuildMST`

### Examples

       # Read two files (Artificially, as we just split 1 file in 2 subsets)
       fileName <- system.file("extdata", "68983.fcs", package="FlowSOM")
       ff1 <- flowCore::read.FCS(fileName)[1:1000,]
       ff1@description$FIL <- "File1"
       ff2 <- flowCore::read.FCS(fileName)[1001:2000,]
       ff2@description$FIL <- "File2"

       flowSOM.res <- FlowSOM(flowCore::flowSet(c(ff1,ff2)), compensate=TRUE,
                              transform=TRUE, scale=TRUE,
                              colsToUse=c(9,12,14:18), maxMeta=10)
       fSOM <- flowSOM.res[[1]]

       # see $metadata for subsets:
       fSOM$metaData

       # Use only the second file, without changing the map
       fSOM2 <- FlowSOMSubset(fSOM,
                              (fSOM$metaData[[2]][1]):(fSOM$metaData[[2]][2]))

[Package FlowSOM version 1.20.0 Index]