[BioC] flowClust results in subset filters

[Florian Hahne]

Hi Bastian,
this is indeed a feature which wasn't implemented yet. I fixed the  
code and everything seems to be working as intended now, but I want to  
give it some more rigorous testing before submitting. I am planning to  
push that back into the release branch since it is more of a bug fix  
than feature addition.
If you want to be more independent of the types of comparisons between  
gating steps, you might want to take a look at the workFlow stuff (as  
described in the package vignette). There you can compute summary  
statistics for a particular gating operation based on another  
reference view in the workFlow (via the additional 'reference'  
argument of the summary method)
bw,
Florian


On 24.04.2009, at 10:30, Bastian Angermann wrote:

> Hi,
>
> I am using R2.9.0 and the 2.4 version of Bioconductor. When I try to  
> run
> a tmixfilter subsetted on a rectangular gate the result is of class  
> logicalFilterResult thus I am unable to access the individual  
> clusters:
> #################################################
> library(flowCore)
> library(flowClust)
> data(rituximab)
>
> r_filter <-  rectangleGate("FSC.H"=c(100,500),"SSC.H"=c(100,500))
> # gate boundaries are not meant to be meaningful.
> t_filter <- tmixFilter("tmix", c("FSC.H", "SSC.H"), K=3)
> result <- filter(rituximab,t_filter %subset% r_filter)
>
> class(result)
> ################################################
>
> Is that a bug, missing feature or am I missing something?
> I'd like to be able to see the result of the
> tmixFilter in the context of the ancestor populations,
> thus the %subset%. I'am working around that by adding an index vector
> to the original flowFrame, to be able to do manual subsetting, but
> it would be nice to to that without this hack.
>
> Thanks a lot,
> Bastian Angermann
> --
>
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