FlowSOMSubset: FlowSOM subset

Description Usage Arguments Value See Also Examples

View source: R/3_buildMST.R

Description

Take a subset from a FlowSOM object

Usage

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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

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   # Read two files (Artificially, as we just split 1 file in 2 subsets)
   fileName <- system.file("extdata","lymphocytes.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. 17, 2017, 10:04 a.m.