R Graphical Manual

Browse All

Last data update: 2014.03.03

R: Brief Information of removed Cell-events by immunoClust...

cell.removed

R Documentation

Brief Information of removed Cell-events by immunoClust Cell-event Clustering

Description

Gives information about the amount of overexposed cell-event observetion in a FCS-file.

Usage

removed.above(fcs, parameters=NULL, N=NULL, max.count=10, max=NULL)
removed.below(fcs, parameters=NULL, N=NULL, min.count=10, min=NULL)

Arguments

`fcs`	An object of class flowFrame. Rows correspond to observations and columns correspond to measured parameters.
`parameters`	A character vector specifying the parameters (columns) to be included in clustering. When it is left unspecified, all the parameters will be used.
`N`	Maximum number of observations used for clustering. When unspecified or higher than the number of observations (i.e. rows) in dat, all observations are used for clustering, otherwise only the first `N` observations.
`max.count`	An integer specifying the threshold count for filtering data points from above. The default is 10, meaning that if 10 or more data points are larger than or equal to `max`, they will be excluded from the analysis. If `max` is `NULL`, then the maximum value of each parameter will be used. To suppress filtering, it is set to -1.
`max`	The upper limit set for data filtering. Note that it is a vector of length equal to the number of parameters (columns), implying that a different value can be set for each parameter.
`min.count`	analoguous to `max.count`.
`min`	analoguous to `min`.

Value

A table with two rows containing the number of events above max in each parameter and above in only this parameter. The two last columns give the sum and percentage of all events above max in any parameter.

Author(s)

Till SÃ¶rensen till-antoni.soerensen@charite.de

Examples

data(dat.fcs)
removed.above(dat.fcs)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

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(immunoClust)
Loading required package: grid
Loading required package: lattice
Loading required package: flowCore
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/immunoClust/cell.removed.Rd_%03d_medium.png", width=480, height=480)
> ### Name: cell.removed
> ### Title: Brief Information of removed Cell-events by immunoClust
> ###   Cell-event Clustering
> ### Aliases: removed.above removed.below
> 
> ### ** Examples
> 
> data(dat.fcs)
> removed.above(dat.fcs)
           FSC-A SSC-A FITC-A PE-A APC-A APC-Cy7-A Pacific Blue-A sum per ttl
above         47   318      0    0     0         0              0 318    3.18
above.only     0   271      0    0     0         0              0 271    2.71
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>