search

federicogiorgi / corto

corto (Correlation Tool): an R package to generate correlation-based DPI networks
20 stars 7 forks source link

Can centroids be Targets? #4

Open pedruru opened 2 years ago

pedruru commented 2 years ago

Dear Federico,

First of all, I would like to thank you for the package that you have developed. I found it quite useful! I noticed that centroids that are found to be Regulators are not included as Targets of other Regulators. What's more, centroids that are not found to be Regulators aren't taken into account as possible Targets. I would like to know if there is a way for centroids to be included as Targets when inferring regulatory networks as I'm interested in this kind of functional interactions. Thank you for your time.

Best regards,

Pedro.

federicogiorgi commented 2 years ago

Hi Pedro!

Thanks for your interest in corto. Your question makes a lot of sense: originally, we wanted corto to distinguish centroids and targets, so that only correlations between the two groups are possible. This allows for a correct execution of the DPI algorithm. However, I believe you can force corto to perform also centroid-centroid relationships, by operating on the input matrix.

For example, if you have centroid variables you want to be included as both targets and centroids, I suggest you duplicate them in the matrix.

For example: gene1 6.5 5.6 7.1

becomes: centroid_gene1 6.5 5.6 7.1 target_gene1 6.5 5.6 7.1

Please let me know how it goes! I have an interest in these hybrid nodes and I am looking forward to the next corto expansion to predict centroid-centroid interactions.

Federico

On Fri, 1 Oct 2021 at 22:38, Pedro Salaberry @.***> wrote:

Dear Federico,

First of all, I would like to thank you for the package that you have developed. I found it quite useful! I noticed that centroids that are found to be Regulators are not included as Targets of other Regulators. What's more, centroids that are not found to be Regulators aren't taken into account as possible Targets. I would like to know if there is a way for centroids to be included as Targets when inferring regulatory networks as I'm interested in this kind of functional interactions. Thank you for your time.

Best regards,

Pedro.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/federicogiorgi/corto/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAKWILBJS433SPAXWQPQQHDUEYL5TANCNFSM5FFOWLNQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.