[maker-devel] keep_preds values

[Carson Holt]

There is a value called abAED being calculated, which somewhat captures
the concordance among the predictors.  It is not currently printed in the
GFF3, but it is used to identify the best non-overlapping ab initio
predictor to put in the non-overlapping fasta file.  There are a couple of
things I still need to do with it to though.  It’s not yet normalized to
take into account the absence of a predictor in the cluster of overlapping
predictions. For example, if I have 2 predictors and 2 make perfectly
matching calls and 1 makes no call, they get a score of 0 before I have
perfect concordance between what’s there, but I really should make it 0.33
because the abscence of the third predictor is meaningful.  The
unnormalized concordance value is fine for deciding which overlapping
model to keep in the file, but not for global comparison.

—Carson



On 3/10/14, 8:08 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
wrote:

>Ok. But that is not implemented no as far as I can tell from the source,
>right? Or is it reflected in the AED for the unsupported models?
>
>Mikael
>
>10 mar 2014 kl. 16:59 skrev Carson Holt <carsonhh at gmail.com>:
>
>> Yes.  It will eventually perform an AED like calculation between
>>multiple
>> predictors (i.e. if you use 3 predictors it, then you require support by
>> at least 2 predictors across all exons to get a value of 0.33).  A value
>> of 0 would be perfect concordance across all 3 predictors.
>> 
>> —Carson
>> 
>> 
>> 
>> 
>> On 3/10/14, 7:57 AM, "Mikael Brandström Durling" <mikael.durling at slu.se>
>> wrote:
>> 
>>> Hi Carson and Daniel,
>>> 
>>> That sounds more logical to me.  Then it would be appropriate to change
>>> the comment of keep_preds in the generated config files.
>>> 
>>> Would it make sense to make keep_preds a non-binary value to evaluate
>>>the
>>> concordance between ab initio models obtained from different
>>>predictors?
>>> That would assume that it is less likely to be a false positive when
>>>two
>>> or more predictors suggest the same unsported model?
>>> 
>>> Mikael
>>> 
>>> 
>>> 10 mar 2014 kl. 16:51 skrev Carson Holt <carsonhh at gmail.com>:
>>> 
>>>> Actually that is false. The keep_preds option is still binary.  Any
>>>> value
>>>> other than 0 sets it to true.  There was discussion about making it a
>>>> non-binary value, but that has not been implemented.
>>>> 
>>>> —Carson
>>>> 
>>>> 
>>>> On 3/10/14, 7:47 AM, "Daniel Ence" <dence at genetics.utah.edu> wrote:
>>>> 
>>>>> Hi Mikael, 
>>>>> 
>>>>> The keep_preds parameter is often used the same as a binary
>>>>>parameter,
>>>>> but it doesn't have to be. The concordance that is mentioned in the
>>>>> comment line is the AED for that prediction. AED is a measurement of
>>>>> how
>>>>> well a prediction is supported by the evidence and ranges from 0 -
>>>>>1. A
>>>>> prediction with an AED of 0 matches the evidence exactly while a
>>>>> prediction with an AED of 1 isn't overlapped by any evidence.
>>>>> 
>>>>> The default behavior for MAKER is to make a gene model out of a
>>>>> prediction with any AED <1. When you change the keep_preds option
>>>>>from
>>>>> 0
>>>>> to 1, then MAKER will make a gene model out of any prediction that
>>>>> matches the other parameters (like single_exon, min_exon, etc).
>>>>>Setting
>>>>> the keep_preds option to somewhere in between 0 and 1 will set a
>>>>> ceiling
>>>>> on the AED required for promoting a prediction to a gene model.
>>>>> 
>>>>> From a user standpoint, when you will almost certainly lose gene
>>>>>models
>>>>> when you set AED at an intermediate value, but you might benefit by
>>>>> knowing that all your models will now have an AED of at least a
>>>>>certain
>>>>> value. 
>>>>> 
>>>>> I hope that helps; let me know if it didn't.
>>>>> 
>>>>> ~Daniel
>>>>> 
>>>>> PS The original paper that described the AED is Eilbeck et al in BMC
>>>>> Bioinformatics 2009. It's also discussed in more detail in the MAKER2
>>>>> paper, the MAKER-P paper, and the Yandell and Ence Nature Reviews
>>>>> Genetics paper from 2012.
>>>>> 
>>>>> Daniel Ence
>>>>> Graduate Student
>>>>> Eccles Institute of Human Genetics
>>>>> University of Utah
>>>>> 15 North 2030 East, Room 2100
>>>>> Salt Lake City, UT 84112-5330
>>>>> ________________________________________
>>>>> From: maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
>>>>> Mikael Brandström Durling [mikael.durling at slu.se]
>>>>> Sent: Monday, March 10, 2014 4:27 AM
>>>>> To: maker-devel at yandell-lab.org
>>>>> Subject: [maker-devel] keep_preds values
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Can someone, please, explain the keep_preds parameter, as it works
>>>>>now
>>>>> with a value between 1 and 0? It used to be binary, but now it seems
>>>>>to
>>>>> test concordance towards something. The maker wiki doesn’t explain it
>>>>> any
>>>>> further either.
>>>>> 
>>>>> Thanks,
>>>>> Mikael
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>> 
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
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>>>>>g
>>>> 
>>>> 
>>> 
>> 
>> 
>