getStats {flowWorkspace}R Documentation

Exact MFI from populations(or nodes) for all the markers

Description

It calculates the MFI for each marker.

Usage

getStats(x, ...)

## S3 method for class 'GatingSetList'
getStats(x, ...)

## S3 method for class 'GatingSet'
getStats(x, ...)

## S3 method for class 'GatingHierarchy'
getStats(x, nodes = NULL, type = "count",
  inverse.transform = FALSE, stats.fun.arg = list(), ...)

Arguments

x

a GatingSet or GatingHierarchy

...

arguments passed to getNodes method.

nodes

the character vector specifies the populations of interest. default is all available nodes

type

the character vector specifies the type of pop stats or a function used to compute population stats. when character, it is expected to be either "count" or "percent". Default is "count" (total number of events in the populations). when a function, it takes a flowFrame object through 'fr' argument and return the stats as a named vector.

inverse.transform

logical flag . Whether inverse transform the data before computing the stats.

stats.fun.arg

a list of arguments passed to ‘type' when ’type' is a function.

Value

a data.table that contains MFI values for each marker per column along with 'pop' column and 'sample' column (when used on a 'GatingSet')

Examples

## Not run: 
dataDir <- system.file("extdata",package="flowWorkspaceData")
suppressMessages(gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)))

# get stats all nodes
dt <- getStats(gs) #default is "count"

nodes <- c("CD4", "CD8")
getStats(gs, nodes, "percent")

# pass a build-in function
getStats(gs, nodes, type = pop.MFI)

# compute the stats based on the raw data scale
getStats(gs, nodes, type = pop.MFI, inverse.transform = TRUE)

# supply user-defined stats fun
pop.quantiles <- function(fr){
   chnls <- colnames(fr)
   res <- matrixStats::colQuantiles(exprs(fr), probs = 0.75)
   names(res) <- chnls
   res
   }
getStats(gs, nodes, type = pop.quantiles)

## End(Not run)

[Package flowWorkspace version 3.30.2 Index]