FlowSOMSubset: FlowSOMSubset

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

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.