[maker-devel] keep_preds values

[Carson Holt]

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
>>> 
>>> 
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>> 
>> 
>