[BioC] flowClust results in subset filters
Kenneth Lo
c.lo at stat.ubc.ca
Wed May 6 01:28:12 CEST 2009
Hi Florian,
Thanks a lot for the fix, which clearly makes the integration of
flowClust with flowCore more sense as now it may tell the class
assignment from tmixFilter when combining its use with other filtering/
gating operations defined in flowCore. I've just checked out the most
updated copy from the devel branch (version 1.11.2), and tried the
example code in your email. The filter method in the 2nd last line of
the example code does return a multipleFilterResult object now, which
is what we desire. However, similar to Bastian's experience, I could
only access the tmixFilter object but not the tmixFilterResult object
in the filterDetails list. Some slots which describe the fitted
distribution using flowClust, e.g., mu, sigma and lambda, are found in
the tmixFilterResult class but not in tmixFilter. Are there any means
to retrieve these pieces of information?
Thanks again,
Kenneth
On 5-May-09, at 11:41 AM, Florian Hahne wrote:
> Hi Bastian, Kenneth,
> the problem in this case is that flowClust extends the
> multipleFilterResult class, adding all the mixture parameters and
> stuff. The subsetFilter operation is defined in flowCore, which
> doesn't really know about all these additional slots. We do have a
> mechanism in place to deal with such cases, i.e, the summarizeFilter
> method which is called whenever a filter is evaluated. This is
> basically just a hook that has access to both the input filter and
> the filterResult, and it can be used to add arbitrary items to the
> filterDetails slot. I added a summarizeFilter method for tmixFilters
> which does exactly that.
> The following will still give you a multipleFilterResult object as
> the result of the subsetFilter operation but now with additional
> flowClust parameters attached in the filterDetails.
>
> library(flowClust)
> data(GvHD)
> foo <- GvHD[[1]]
> rg <- rectangleGate("FSC-H"=c(100,600), "SSC-H"=c(200, 700))
> tm <- tmixFilter(parameters=c("FSC-H", "SSC-H"), K=3)
> fr <- filter(foo, tm %subset% rg)
> names(filterDetails(fr, "tmixFilter in defaultRectangleGate"))
>
> Note that there are three items in the filterDetails list, one for
> each of the components of the subsetFilter and one for the
> subsetFilter itself, and that the latter contains copies of values
> of the former two. This is intentional, albeit a bit unfortunate in
> this case, since the additional flowClust parameters contain a lot
> of information (large matrices, indexing vectors...), which is
> unnecessarily copied here.
>
> bw,
> Florian
>
>
> Bastian Angermann wrote:
>> Thank you very much and have a great weekend.
>>
>> Bastian
>>
>> -------- Original-Nachricht --------
>>
>>> Datum: Fri, 01 May 2009 14:16:01 -0700
>>> Von: Florian Hahne <fhahne at fhcrc.org>
>>> An: Bastian Angermann <AngerB at gmx.de>
>>> Betreff: Re: [BioC] flowClust results in subset filters
>>>
>>
>>
>>> Ok, I will take a look asap,
>>> Florian
>>>
>>> Bastian Angermann wrote:
>>>
>>>> Hi Florian,
>>>>
>>>> I've come over a minor issue with the current return type of a
>>>> filter operation that subsets a tmix-filter within an other filter.
>>>>
>>>> While the current return type of multipleFilterResult allows to
>>>> access
>>>> the class assignment by the tmix-Filter, the results describing
>>>> the fitted distribution (i.e. means, proportions and covariance
>>>> matrices) are not accessible. The filter included in the
>>>>
>>> filterDetails in the appropriate gate is of type tmixFilter and not
>>> tmixFilterResult, which would of course have a redundant subSet.
>>>> Access to the parameters of the fitted distributions would be
>>>> quite usefull.
>>>>
>>>> Best,
>>>> Bastian
>>>> -------- Original-Nachricht --------
>>>>
>>>>> Datum: Mon, 27 Apr 2009 17:41:43 -0700
>>>>> Von: Florian Hahne <fhahne at fhcrc.org>
>>>>> An: Bastian Angermann <AngerB at gmx.de>
>>>>> Betreff: Re: [BioC] flowClust results in subset filters
>>>>>
>>>>
>>>>> Hi Bastian,
>>>>> I just committed the changes to the devel branch of the package
>>>>>
>>> (version
>>>>> 1.11.1).
>>>>> It might take a day or two to build, but it would be great if
>>>>> you could
>>>>> take a look at this version first. I would like to hold off on
>>>>> bumping things back into release unless we are all happy with it.
>>>>> If you know how to build the devel package from source you
>>>>> should be able to get the 1.11.1 version as of now.
>>>>> Florian
>>>>>
>>>>> Bastian Angermann wrote:
>>>>>
>>>>>> Hi Florian,
>>>>>>
>>>>>> thanks for your reply. Let me know if I can do any beta testing
>>>>>> of the new code.
>>>>>>
>>>>>> Cheers,
>>>>>> Bastian.
>>>>>> -------- Original-Nachricht --------
>>>>>>
>>>>>>> Datum: Sun, 26 Apr 2009 22:49:02 -0700
>>>>>>> Von: Florian Hahne <fhahne at fhcrc.org>
>>>>>>> An: Bastian Angermann <AngerB at gmx.de>
>>>>>>> CC: Bioconductor at stat.math.ethz.ch
>>>>>>> Betreff: Re: [BioC] flowClust results in subset filters
>>>>>>>
>>>>>>
>>>>>>> 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
>>>>>>>> --
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Bioconductor mailing list
>>>>>>>> Bioconductor at stat.math.ethz.ch
>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>>>> Search the archives:
>>>>>>>>
>>>>>>> http://news.gmane.org/
>>>>>>> gmane.science.biology.informatics.conductor
>>>>>>>
>>>>>>
>>>>> --
>>>>> 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
>>>>>
>>>>
>>> --
>>> 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
>>>
>>
>>
>
>
> --
> 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
>
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