FlowSOMSubset: FlowSOM subset

In FlowSOM: Using self-organizing maps for visualization and interpretation of cytometry data

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]))

FlowSOM documentation built on Nov. 8, 2020, 6:40 p.m.