'cytoFrame': a class for storing observed quantitative properties from a population of cells, most likely from a FACS run or, alternatively, from automated microscopy

Description

This class represents the data contained in a FCS 3.0 file or similar data structures.

Details

Although objects of class cytoFrame can be used to hold arbitrary data of cell populations, the main focus lies on flow-cytometry data.

FCS 3.0 is the Data File Standard for Flow Cytometry, Version FCS3.0. See the vignette of this package for additional information on using the object system for handling of flow-cytometry data.

Creating Objects

Objects can be created using
new('cytoFrame',
exprs = ...., # Object of class matrix
description = .... # Object of class character
)
or the function readFCS.

Slots

exprs:

Object of class matrix containing the measured intensities. Rows correspond to cells, columns to the different channels. The colnames attribute of the matrix is supposed to hold the names or identifiers for the channels. The rownames attribute would usually not be set.

description:

A named character vector containing the experiment description as key-value pairs.

well:

A single integer vector giving the position of the well on a microtitre plate. This only applies when using the object within a cytoSet collection and will usually be filled in by the function readCytoSet.

gate:

An object of class gateSet. This object can be used to select defined subsets of the data, a process referred to as gating in the analysis of flow-cytometry data.

Methods

[

subsetting. Returns an object of class cytoFrame. The subsetting is applied to the exprs slot, while the description slot is unchanged.

exprs, exprs<-

extract or replace the intensities.

description, description<-

extract or replace the description.

show

display summary.

plot

scatterplot for cytoFrame objects. The additional argument gate can be used to plot subsets of the data defined by either an object of class gate or by a character vector giving the name of one of the gates in the list.

gate,gate<-

extract or replace the list of gates.

ncol,nrow

extract the dimensions of the data matrix.

appendGate

Append a gate or gateSet to the gate slot.

drawGate

Create an object of class gate or gateSet based on a selection made from the data.

hist

Draw a histogram of the data

Author(s)

Florian Hahne, Wolfgang Huber

See Also

readFCS, cytoSet, gate, gateSet

Examples

intens <- matrix(runif(100), ncol=4)
colnames(intens) <- c("FL1-H", "FL2-H", "FL3-H", "FL4-H")

a <- new("cytoFrame",
          exprs=intens,
          description=c(name="example data", date=date()))

description(a)
dim(exprs(a))           

a[1:3, -4]

plot(a)
## Not run: 
g1 <- drawGate(a, name="Gate1")

## End(Not run)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(prada)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: RColorBrewer
Loading required package: grid
Loading required package: rrcov
Loading required package: robustbase

Attaching package: 'robustbase'

The following object is masked from 'package:Biobase':

    rowMedians

Scalable Robust Estimators with High Breakdown Point (version 1.3-11)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/prada/cytoFrame-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cytoFrame-class
> ### Title: 'cytoFrame': a class for storing observed quantitative
> ###   properties from a population of cells, most likely from a FACS run
> ###   or, alternatively, from automated microscopy
> ### Aliases: cytoFrame-class cytoFrame [,cytoFrame,ANY,ANY,ANY-method
> ###   description,cytoFrame-method description<-,cytoFrame,character-method
> ###   exprs,cytoFrame-method exprs<-,cytoFrame,matrix-method
> ###   colnames,cytoFrame-method colnames<-,cytoFrame-method
> ###   show,cytoFrame-method plot,cytoFrame,missing-method $.cytoFrame
> ###   gate,cytoFrame-method gate<-,cytoFrame,gate-method
> ###   gate<-,cytoFrame,gateSet-method drawGate,cytoFrame-method
> ###   drawGate,cytoFrame-method drawGate,matrix-method
> ###   appendGates,cytoFrame-method ncol,cytoFrame-method
> ###   nrow,cytoFrame-method applyGate,cytoFrame,gate-method
> ###   applyGate,cytoFrame,gateSet-method
> ###   applyGate,cytoFrame,character-method
> ###   applyGate,cytoFrame,numeric-method applyGate,cytoFrame,logical-method
> ###   hist,cytoFrame-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> intens <- matrix(runif(100), ncol=4)
> colnames(intens) <- c("FL1-H", "FL2-H", "FL3-H", "FL4-H")
> 
> a <- new("cytoFrame",
+           exprs=intens,
+           description=c(name="example data", date=date()))
> 
> description(a)
                      name                       date 
            "example data" "Thu Jul  7 02:40:03 2016" 
> dim(exprs(a))           
[1] 25  4
> 
> a[1:3, -4]
cytoFrame object with 3 cells and 3 observables:
FL1-H FL2-H FL3-H
slot 'description' has 2 elements
> 
> plot(a)
> ## Not run: 
> ##D g1 <- drawGate(a, name="Gate1")
> ## End(Not run)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>