GetThresholdedIntensities {COMPASS} | R Documentation

## Extract Thresholded Intensities from a GatingSet

### Description

This function extracts thresholded intensities for children of a node `node`, as specified through the `map` argument.

### Usage

    GetThresholdedIntensities(gs, node, map)

### Arguments

`gs` | A `GatingSet` or `GatingSetList`.
`node` | The name, or path, of a single node in a `GatingSet` / `GatingSetList`.
`map` | A `list`, mapping node names to markers.

### Details

`map` should be an R `list`, mapping node names (as specified in the gating hierarchy of the gating set) to channel names (as specified in either the `desc` or `name` columns of the parameters of the associated `flowFrame`s in the `GatingSet`).

### Value

A `list` with two components:

`data` | A `list` of thresholded intensity measures.
`counts` | A named vector of total cell counts at the node `node`.

### Examples

    if (require("flowWorkspace")&require("flowCore")&require("tidyr")) {

      ## Generate an example GatingSet that could be used with COMPASS
      ## We then pull out the 'data' and 'counts' components that could
      ## be used within a COMPASSContainer

      n <- 10 ## number of samples
      k <- 4 ## number of markers

      sid_vec <- paste0("sid_", 1:n) ## sample ids; unique names used to denote samples
      iid_vec <- rep_len( paste0("iid_", 1:(n/10) ), n ) ## individual ids
      marker_names <- c("TNFa", "IL2", "IL4", "IL6")

      ## Generate n sets of 'flow' data -- a list of matrices, each row
      ## is a cell, each column is fluorescence intensities on a particular
      ## channel / marker
      data <- replicate(n, {
        nrow <- round(runif(1) * 1E4 + 1000)
        ncol <- k
        vals <- rexp( nrow * ncol, runif(1, 1E-5, 1E-3) )
        output <- matrix(vals, nrow, ncol)
        colnames(output) <- marker_names
        return(output)
      })
      names(data) <- sid_vec

      ## Put it into a GatingSet
      fs <- flowSet( lapply(data, flowFrame) )
      gs <- GatingSet(fs)

      ## Add some dummy metadata
      meta <- pData(gs)
      meta$PTID <- 1:10
      pData(gs) <- meta

      gate <- rectangleGate( list(TNFa=c(-Inf,Inf)))
      gs_pop_add(gs, gate, parent="root", name="dummy")

      ## Add dummy gate

      ## Make some gates, and apply them
      invisible(lapply(marker_names, function(marker) {
        .gate <- setNames( list( c( rexp(1, runif(1, 1E-5, 1E-3)), Inf) ), marker )
        gate <- rectangleGate(.gate=.gate)
        gs_pop_add(gs, gate, parent="dummy", name=paste0(marker, "+"))
      }))

      recompute(gs)

      ## Map node names to channel names
      map=list(
        "TNFa+"="TNFa",
        "IL2+"="IL2",
        "IL4+"="IL4",
        "IL6+"="IL6"
      )

      ## Pull out the data as a COMPASS-friendly dataset
      node <- "dummy"
      map <- map
      system.time(
        output <- GetThresholdedIntensities(gs, "dummy", map)
      )

      system.time(
        output <- COMPASSContainerFromGatingSet(gs, "dummy", individual_id="PTID")
      )

      str(output)

    }

[Package COMPASS version 1.30.0 Index]