First of all thank you for this package is amazing the things that you can do.
I already installed the package into a virtual environment working fine with default parameters. But, I wanted to add new parameters such as a specific gene list separated by line ("-g") and "-K 4" to increase the pair genes and in my case i want to analiyse for 4 genes .
Command used:
Comet -C 20 -K 4 -g ./gene_list.txt ./tabmaker_RNA.txt ./tabvis.txt ./tabcluster.txt output_within_ManualSelectedCells_4PairGenes/
This runs through without any errors. So I was checking the csv files for each cluster and found out that the cluster_X_quads.csv has gene combination repetition (table attached) and to my understanding this shouldnt be possible as it is supposed to get eliminated as your paper state "Duplicates and gene-repeating combinations are once again filtered out, and the resulting entries contain unique 4 gene marker panels." in the materials and methods section "Computing and ranking 4-gene marker panels".
Is there something that i am missing in the interpretation, or parameters or something
Thank you in advanced
cluster_4_quads_sample.csv
First of all thank you for this package is amazing the things that you can do.
I already installed the package into a virtual environment working fine with default parameters. But, I wanted to add new parameters such as a specific gene list separated by line ("-g") and "-K 4" to increase the pair genes and in my case i want to analiyse for 4 genes .
Command used:
Comet -C 20 -K 4 -g ./gene_list.txt ./tabmaker_RNA.txt ./tabvis.txt ./tabcluster.txt output_within_ManualSelectedCells_4PairGenes/
This runs through without any errors. So I was checking the csv files for each cluster and found out that the cluster_X_quads.csv has gene combination repetition (table attached) and to my understanding this shouldnt be possible as it is supposed to get eliminated as your paper state "Duplicates and gene-repeating combinations are once again filtered out, and the resulting entries contain unique 4 gene marker panels." in the materials and methods section "Computing and ranking 4-gene marker panels".
Is there something that i am missing in the interpretation, or parameters or something
Thank you in advanced
cluster_4_quads_sample.csv