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Clarify mapping of rules to traits? #10

Closed andrewd789 closed 11 months ago

andrewd789 commented 1 year ago

Hello,

Thanks for the great package. I have applied microtrait to several metagenomes. Now I wish to interpret the rules and traits detected, but I am puzzled by some aspects of this.

I downloaded the supplementary excel tables from the microtraits publication (https://www.frontiersin.org/articles/10.3389/fbinf.2022.918853/full), to try to determine how the rules and traits matched up with one another. I see that there are 1,445 rules listed (in ST4), but only 975 rules are listed in the rules-to-traits mapping (in ST5). What explains this difference, and how can one interpret the rules not listed in the rules-to-traits mapping?

Thanks,

Andrew.

ukaraoz commented 12 months ago

Thanks Andrew. The primary output of microtrait is the trait matrix, which captures a subset of the asserted rules as you said. The other rules are there for mostly debugging specificity/sensitivity tradeoff for those assertions. They mostly map to the same traits in the trait matrix where the stringency of the detection is different (i.e. more/less stringent co-occurrence of the protein families to assert detection of a pathway). ulas.

Ulas Karaoz, Ph.D. Research Scientist Climate and Ecosystems Sciences Lawrence Berkeley National Laboratory

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On Fri, Sep 8, 2023 at 3:21 AM Andrew D @.***> wrote:

Hello,

Thanks for the great package. I have applied microtrait to several metagenomes. Now I wish to interpret the rules and traits detected, but I am puzzled by some aspects of this.

I downloaded the supplementary excel tables from the microtraits publication ( https://www.frontiersin.org/articles/10.3389/fbinf.2022.918853/full), to try to determine how the rules and traits matched up with one another. I see that there are 1,445 rules listed (in ST4), but only 975 rules are listed in the rules-to-traits mapping (in ST5). What explains this difference, and how can one interpret the rules not listed in the rules-to-traits mapping?

Thanks,

Andrew.

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andrewd789 commented 11 months ago

Hi, many thanks for the explanation. I will focus on the rules represented in the rule-to-traits table then.

A.