FlowSOM (version 1.0.0)

FlowSOMSubset: 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

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","lymphocytes.fcs",package="FlowSOM")
    ff1 <- read.FCS(fileName)[1:1000,]
    ff1@description$FIL <- "File1"
    ff2 <- read.FCS(fileName)[1001:2000,]
    ff2@description$FIL <- "File2"
    
    flowSOM.res <- FlowSOM(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]))