FlowSOMSubset {FlowSOM} | R Documentation

## FlowSOMSubset

### Description

FlowSOM subset

### Usage

    FlowSOMSubset(fsom, ids)

### Arguments

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

### Details

Take a subset from a FlowSOM object

### 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, ]
       flowCore::keyword(ff1)[["FIL"]] <- "File1"
       ff2 <- flowCore::read.FCS(fileName)[1001:2000, ]
       flowCore::keyword(ff2)[["FIL"]] <- "File2"

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

       # see $metadata for subsets:
       flowSOM.res$metaData

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

[Package FlowSOM version 2.2.0 Index]