FlowSOMSubset {FlowSOM} | R Documentation |
FlowSOM subset
FlowSOMSubset(fsom, ids)
fsom |
FlowSOM object, as generated by |
ids |
Array containing the ids to keep |
Take a subset from a FlowSOM object
FlowSOM object containg updated data and medianvalues, but with the same grid
# 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]))