gs_pop_get_count_fast: Return a table of population statistics for all populations...

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

Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy

Description

gs_pop_get_count_fast is more useful than getPop. Returns a table of population statistics for all populations in a GatingHierarchy/GatingSet. Includes the xml counts, openCyto counts and frequencies.

Usage

gs_pop_get_count_fast(
  x,
  statistic = c("count", "freq"),
  xml = FALSE,
  subpopulations = NULL,
  format = c("long", "wide"),
  path = "full",
  ...
)

gs_pop_get_count_with_meta(x, ...)

Arguments

x	a GatingSet or GatingSetList
statistic	character specifies the type of population statistics to extract.(only valid when format is "wide"). Either "freq" or "count" is currently supported.
xml	logical indicating whether the statistics come from xml (if parsed from xml workspace) or from openCyto.
subpopulations	character vector to specify a subset of populations to return. (only valid when format is "long")
format	character value of c("wide", "long") specifing whether to origanize the output in long or wide format
path	character see gs_get_pop_paths
...	additional arguments passed to gs_pop_get_count_fast

Details

gs_pop_get_count_fast returns a table population statistics for all populations in the gating hierarchy. The output is useful for verifying that the import was successful, if the xml and openCyto derived counts don't differ much (i.e. if they have a small coefficient of variation.) for a GatingSet, returns a matrix of proportions for all populations and all samples

Value

gs_pop_get_count_fast returns a data.frame with columns for the population name, xml derived counts, openCyto derived counts, and the population proportions (relative to their parent pouplation).

a data.table of merged population statistics with sample metadata.

See Also

gs_get_pop_paths

Examples

        ## Not run: 
        #gh is a GatingHierarchy
        gs_pop_get_count_fast(gh);
        gh_pop_get_stats(gh,gs_get_pop_paths(gh,tsort=T)[5])

        #gs is a GatingSet
        gs_pop_get_count_fast(gs)
        #optionally output in long format as a data.table
        gs_pop_get_count_fast(gs, format = "long", path = "auto")
        #only get stats for a subset of populations
        gs_pop_get_count_fast(gs, format = "long", subpopulations = gs_get_pop_paths(gs)[4:6])
        
## End(Not run)
 ## Not run: 
    #G is a GatingSetList
    stats = gs_pop_get_count_with_meta(G)
  
## End(Not run)

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