filterSummary-class: Class "filterSummary"

In RGLab/flowCore: flowCore: Basic structures for flow cytometry data

Class "filterSummary"

Description

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

Usage

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

Arguments

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

Details

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

Value

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.

Slots

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 from the Class

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

Methods

[[

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.

Author(s)

Florian Hahne, Byron Ellis

See Also

filterResult, logicalFilterResult, multipleFilterResult, flowFrame filterSummaryList

Examples

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)

RGLab/flowCore documentation built on Aug. 26, 2024, 8:52 a.m.