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saezlab / cosmosR

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.
https://saezlab.github.io/cosmosR/
GNU General Public License v3.0
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Is it possible to run COSMOS without metabolic data? #22

Closed kaupuks closed 1 year ago

kaupuks commented 1 year ago

Could you provide an example how to run COSMOS without metabolic data, only with TF and kinase activity estimation? Tried without succes preprocess_COSMOS_signaling_to_metabolism (signaling_data = c(kinase_activity_input, tf_activity_input),metabolic_data = NULL) and etc.

Thank in advance Algirdas

adugourd commented 1 year ago

Hi,

in theory if the data is in the correct format, it should work if you do

preprocess_COSMOS_signaling_to_metabolism (signaling_data = kinase_activity_input, metabolic_data = tf_activity_input)

The idea is to use one of the two (TF or kinase) instead of metabolomic. Essentially COSMOS try to find connections between whatever is provided as signaling_data and metabolic_data. It is very flexible with the actual content of the variable, as long as they can be mapped on the meta_network.

Cheers,

Aurelien

kaupuks commented 1 year ago

great, thank you!