readFCS: Read an FCS file

In prada: Data analysis for cell-based functional assays

Description

Read one or several FCS files: Data File Standard for Flow Cytometry

Usage

  read.fcs(filename=NULL, objectModel="prada", ...)
  readFCS(filename)

Arguments

filename	Character of length 1: filename
objectModel	Character of length 1: the object model to use for the output. Curently only 'prada' for cytoFrame objects is supported.
...	Arguments that get passed on to higher-level import functions.

Details

The function readFCS works with the output of the FACS machine software from a number of vendors. However, the FCS 3.0 standard includes some options that are not yet implemented in this function. If you need extensions, please let me know. The output of the fucntion is an object of class cytoFrame.

read.fcs is a wrapper function that allows the user to specify the class of the output. The purpose of the function is to standardize the way flow cytometry data is imported into R using the prada package. If the filename argument to read.fcs is a character vector of length > 1, multiple FCS files can be imported. Please see the documentation for readCytoSet for alternatives ways to import multiple FCS files and for more details on the higher-level import function.

For specifications of FCS 3.0 see http://www.isac-net.org and the file ../doc/fcs3.html in the doc directory of the package.

Value

An object of class cytoFrame.

Author(s)

Wolfgang Huber http://www.ebi.ac.uk/huber, Florian Hahne

See Also

readCytoSet

Examples

sampdat <- readFCS(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                               package="prada"))
files <- dir(system.file("extdata", package="prada"),
             pattern="[A-H][0-9][0-9]")
sampdat2 <- read.fcs(system.file("extdata", "fas-Bcl2-plate323-04-04.A01",
                               package="prada"))
sampdat3 <- read.fcs(files, path=system.file("extdata", package="prada"))
sampdat
exprs(sampdat[1:3,])
description(sampdat)[3:6]
class(sampdat3)

Example output

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, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, 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, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

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 1.4-3)

cytoFrame object with 2115 cells and 8 observables:
FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
slot 'description' has 148 elements
     FSC-H SSC-H FL1-H FL2-H FL3-H FL2-A FL4-H Time
[1,]   467   532    87   146    14     0   449    2
[2,]   437   431    28   145    16     0   478    2
[3,]   410   214     0    30     7     0   358    2
                        $NEXTDATA                              $SYS 
                              "0" "Macintosh System Software 9.2.2" 
                          CREATOR                              $TOT 
           "CellQuest Pro  4.0.2"                            "2115" 
[1] "cytoSet"
attr(,"package")
[1] "prada"

prada documentation built on April 28, 2020, 7:52 p.m.