FlowSOMSubset: FlowSOMSubset

View source: R/3_buildMST.R

FlowSOMSubsetR 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 containing updated data and median values, 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]))


saeyslab/FlowSOM documentation built on July 6, 2024, 10:59 a.m.