[maker-devel] keep_preds values

[Carson Holt]

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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