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.

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

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.

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

See also

Examples

if (FALSE) { #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]) } if (FALSE) { #G is a GatingSetList stats = gs_pop_get_count_with_meta(G) }