gs_pop_get_stats: Extract stats from populations(or nodes)

In RGLab/flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Extract stats from populations(or nodes)

Description

Extract stats from populations(or nodes)

Usage

gs_pop_get_stats(x, ...)

gh_pop_get_stats(
  x,
  nodes = NULL,
  type = "count",
  xml = FALSE,
  inverse.transform = FALSE,
  stats.fun.arg = list(),
  ...
)

Arguments

x	a GatingSet or GatingHierarchy
...	arguments passed to gs_get_pop_paths 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.
xml	whether to extract xml stats or openCyto stats
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 stats values (if MFI, 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 <- gs_pop_get_stats(gs) #default is "count"

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

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

# compute the stats based on the raw data scale
gs_pop_get_stats(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
   }
gs_pop_get_stats(gs, nodes, type = pop.quantiles)

## End(Not run)

RGLab/flowWorkspace documentation built on March 17, 2024, 2:24 p.m.