[BioC] flowCore::parameters

[Florian Hahne]

Hi Bastian,
I just fixed this issue in the devel branch. Note that you will need to 
update both flowCore and flowClust. There have been substantial changes 
to the way things were handled compared to the previous release, so it 
would be tedious to port this fix back into the release branch.

In the meantime, evaluating this before calling the parameters method 
should fix the issue in a sort of hackish way:

setMethod("parameters",
          signature=signature(object="filterResult"),
          definition=function(object)
          unique(unlist(sapply(filterDetails(object),
                               function(x) if(is.list(x)) x$parameters))))

Thanks for reporting the issue,
Florian


Bastian Angermann wrote:
> Hi list,
>
> I am having trouble with the parameters method in flowCore. When applying parameters to an element of multipleFilterResult generated by a tmixFilter, R will throw the following error:
> Error in x$parameters : $ operator is invalid for atomic vectors
>
> This came up while trying to apply an other filter to the result of a tmixFilter.
>
> Best,
> Bastian Angermann
>
> Here's how to reproduce the error (R 2.9.0 flowCore SVN 39752 /flowClust SVN 39598):
>
> data(GvHD)
> fcsData <- GvHD[[1]]
>
> tmixGate <- tmixFilter(parameters=c("FSC-H","SSC-H"), K=1)
>
> recGate <- rectangleGate(.gate=list("FSC-H"=c(0,1000),"SSC-H"=c(0,1000)))
> rf <- filter(fcsData,recGate)
> tf <-filter(fcsData,tmixGate %subset% rf )
>
>   
>> tf
>>     
> A filterResult produced by the filter named 'tmixFilter in defaultRectangleGate'
>  resulting in multiple populations:
>          1
>   
>> class(tf)
>>     
> [1] "multipleFilterResult"
> attr(,"package")
> [1] "flowCore"
>   
>> parameters(tf)
>>     
> [1] "FSC-H" "SSC-H"
>   
>> parameters(tf[[1]])
>>     
> Error in x$parameters : $ operator is invalid for atomic vectors
>
>
>
>
>   


-- 
Florian Hahne, PhD
Computational Biology Program
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-3148
fhahne at fhcrc.org