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petitmingchang / TO-GCN

Pipeline of time-ordered gene coexpression network (TO-GCN) construction from three-dimensional (gene expression, condition, and time) data
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README.md has errors in commands #5

Closed ckeeling closed 1 year ago

ckeeling commented 4 years ago

(2) GCN: Constructing eight GCNs for different types

GCN 13 13 example_data/TFs_1718.tsv example_data/TFs_1718.tsv 0.84 0.84 -0.75 -0.75

Should be:

GCN 13 13 example_data/TFs_1718.tsv example_data/All_genes_25489.tsv 0.83 0.83 -0.76 -0.73

And, (3) TO-GCN: Determining time-ordered level in the interesting GCN

TO-GCN 13 13 example_data/TFs_1718.tsv example_data/TFs_1718.tsv 0.84 0.84 example_data/seeds.txt 0

Should be:

TO-GCN 13 13 example_data/TFs_1718.tsv example_data/All_genes_25489.tsv 0.84 0.84 example_data/seeds.txt 0
petitmingchang commented 4 years ago

Thanks for your comment. For (2) to construction the gene coexpression network (GCN), it depends what relationship you want. If you want to know the coexpression relationship between TF and all genes, you can use the second command you showed. However, if you only want to get the GCN among TFs, please use the original command. For (3) to determine the time-ordered level of GCN, we should use the original command. Please take a look at the reference paper and you will know the reason.