filterSummary-class: Class "filterSummary"
In flowCore: flowCore: Basic structures for flow cytometry data

Description Usage Arguments Details Value Slots Objects from the Class Methods Author(s) See Also Examples

Class and methods to handle the summary information of a gating operation.

1 2	## S4 method for signature 'filterResult' summary(object, ...)

`object`	An object inheriting from class `filterResult` which is to be summarized.
`...`	Further arguments that are passed to the generic.

Calling summary on a filterResult object prints summary information on the screen, but also creates objects of class filterSummary for computational access.

An object of class filterSummary for the summary constructor, a named list for the subsetting operators. The $ operator returns a named vector of the respective value, where each named element corresponds to one sub-population.

name: Object of class "character" The name(s) of the populations created in the filtering operation. For a logicalFilterResult this is just a single value; the name of the link{filter}.
true: Object of class "numeric". The number of events within the population(s).
count: Object of class "numeric". The total number of events in the gated flowFrame.
p: Object of class "numeric" The percentage of cells in the population(s).

Objects are created by calling summary on a link{filterResult} object. The user doesn't have to deal with manual object instantiation.

[[: signature(x = "filterSummary", i = "numeric"): Subset the filterSummary to a single population. This only makes sense for multipleFilterResults. The output is a list of summary statistics.
[[: signature(x = "filterSummary", i = "character"): see above
$: signature(x = "filterSummary", name = "ANY"): A list-like accessor to the slots and more. Valid values are n and count (those are identical), true and in (identical), false and out (identical), name, p and q (1-p).
coerce: signature(from = "filterSummary", to = "data.frame"): Coerce object to data.frame.
length: signature(x = "filterSummary"): The number of populations in the fitlerSummary.
names: signature(x = "filterSummary"): The names of the populations in the filterSummary.
print: signature(x = "filterSummary"): Print details about the object.
show: signature(object = "filterSummary"): Print details about the object.
toTable: signature(x = "filterSummary"): Coerce object to data.frame.

Florian Hahne, Byron Ellis

filterResult, logicalFilterResult, multipleFilterResult, flowFrame filterSummaryList

library(flowStats)

## Loading example data, creating and applying a curv1Filter
dat <- read.FCS(system.file("extdata","0877408774.B08",
package="flowCore"))
c1f <- curv1Filter(filterId="myCurv1Filter", x=list("FSC-H"), bwFac=2)
fres <- filter(dat, c1f)

## creating and showing the summary
summary(fres)
s <- summary(fres)

## subsetting
s[[1]]
s[["peak 2"]]

##accessing details
s$true
s$n
toTable(s)