gs_pop_get_stats {flowWorkspace} | R Documentation |
Extract stats from populations(or nodes)
gs_pop_get_stats(x, ...) gh_pop_get_stats( x, nodes = NULL, type = "count", xml = FALSE, inverse.transform = FALSE, stats.fun.arg = list(), ... )
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. |
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')
## 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)